Diffusion activation energy versus the favourable energy in two-order-parameter model:A molecular dynamics study of liquid Al

In the present work, we find that both diffusion activation energy Ea（D） and Ea（S^ex） increase linearly with pressure and have the same slope （0.022±0.001 eV/GPa） for liquid Al. The temperature and pressure dependence of excess entropy is well fitted by the expression -S^ex （T, P）/kB = a（P）＋ b（P）T ＋ c（P） exp（Ef/kBT）, which together with the small ratio of Ef/kB T leads to the relationship of excess entropy to temperature and pressure, i.e. Sex ~ -cEf/T, where c is about 12 and Ef （= △E - P△V） is the favourable energy. Therefore, there exists a simple relation between Ea（S^ex） and Ef, i.e. Ea（S^ex） ≈ cEf.

Molecular Dynamics, Diffusion Coefficients and Activation Energy of the Electrolyte (Anode) in Lithium (Li and Li+), Sodium (Na and Na+) and Potassium (K and K+)

This work is a simulation modelling with the LAMMPS calculation code of an electrode based on alkali metals (lithium, sodium and potassium) using the MEAM potential. For different multiplicities, two models were studied;with and without gap. In this work, we present the structural, physical and chemical properties of the lithium, sodium and potassium electrodes. For the structural properties, the cohesive energy and the mesh parameters were calculated, revealing that, whatever the chemical element selected, the compact hexagonal hcp structure is the most stable, followed by the face-centred cubic CFC structure, and finally the BCC structure. The most stable structure is lithium, with a cohesion energy of -6570 eV, and the lowest bcc-hcp transition energy of -0.553 eV/atom, followed by sodium. For physical properties, kinetic and potential energies were calculated for each of the sectioned chemical elements, with lithium achieving the highest value. Finally, for the chemical properties, we studied the diffusion coefficient and the activation energy. Only potassium followed an opposite order to the other two, with the quantities with lacunae being greater than those without lacunae, whatever the multiplicity. The order of magnitude of the diffusion coefficients is given by the relationship DLi > DNa > Dk for the multiplicity 6*6*6, while for the activation energy the order is reversed.

Molecular Dynamics, Physical Properties, Diffusion Coefficients and Activation Energy of the Lithium Oxide (Li-O) and Sodium Oxide (Na-O) Electrolyte (Cathode)

This work is a simulation model with the LAMMPS calculation code of an electrode based on alkali metal oxides (lithium, sodium and potassium) using the Lennard Jones potential. For a multiplicity of 8*8*8, we studied a gap-free model using molecular dynamics. Physical quantities such as volume and pressure of the Na-O and Li-O systems exhibit similar behaviors around the thermodynamic ensembles NPT and NVE. However, for the Na2O system, at a minimum temperature value, we observe a range of total energy values;in contrast, for the Li2O system, a minimum energy corresponds to a range of temperatures. Finally, for physicochemical properties, we studied the diffusion coefficient and activation energy of lithium and potassium oxides around their melting temperatures. The order of magnitude of the diffusion coefficients is given by the relation Dli-O >DNa-O for the multiplicity 8*8*8, while for the activation energy, the order is well reversed EaNa-O > EaLi-O.

Investigation of Projectile Impact Behaviors of Graphene Aerogel Using Molecular Dynamics Simulations

Graphene aerogel(GA),as a novel solid material,has shown great potential in engineering applications due to its unique mechanical properties.In this study,the mechanical performance of GA under high-velocity projectile impacts is thoroughly investigated using full-atomic molecular dynamics(MD)simulations.The study results show that the porous structure and density are key factors determining the mechanical response of GA under impact loading.Specifically,the impact-induced penetration of the projectile leads to the collapse of the pore structure,causing stretching and subsequent rupture of covalent bonds in graphene sheets.Moreover,the effects of temperature on the mechanical performance of GA have been proven to be minimal,thereby highlighting the mechanical stability of GA over a wide range of temperatures.Finally,the energy absorption density(EAD)and energy absorption efficiency(EAE)metrics are adopted to assess the energy absorption capacity of GA during projectile penetration.The research findings of this work demonstrate the significant potential of GA for energy absorption applications.

Molecular Docking, 3D-QSAR and Molecular Dynamics Simulation Studies of Substituted Pyrimidines as Selective Covalent Janus Kinase 3 Inhibitors

Janus kinase 3（JAK3） is a member of Janus kinase（JAK） family, and it represents a promising target for the treatment of immune diseases and cancers. However, no highly selective inhibitors of JAK3 have been developed. For discovering the binding mechanism of JAK3 and these inhibitors, a molecular modeling study combining molecular docking, three-dimensional quantitative structure-activity relationships（3D-QSAR）, molecular dynamics and binding free energy calculations was performed on a series of pyrimidine-based compounds which could bind with the unique residue Cys909 of JAK3 kinase as the selective inhibitors of JAK3 in this work. The optimum Co MFA and Co MSIA models were generated based on the conformations obtained by molecular docking. The results showed that the models have satisfactory predicted capacity in both internal and external validation. Furthermore, a 50 ns molecular dynamics simulation was carried out to determine the detailed binding process of inhibitors with different activities. It was demonstrated that hydrogen bond interactions with Leu828, Glu903, Tyr904, Leu905 and Leu956 of JAK3 are significant for activity increase, and the Van der Waals interaction is mainly responsible for stable complex.

Surface diffusion of Si, Ge and C adatoms on Si (001) substrate studied by the molecular dynamics simulation

Depositions of Si, Ge and C atoms onto a preliminary Si （001） substrate at different temperatures are investigated by using the molecular dynamics method. The mechanism of atomic self-assembling occurring locally on the flat terraces between steps is suggested. Diffusion and arrangement patterns of adatoms at different temperatures are observed. At 900 K, the deposited atoms are more likely to form dimers in the perpendicular [110] direction due to the more favourable movement along the perpendicular [110] direction. C adatoms are more likely to break or reconstruct the dimers on the substrate surface and have larger diffusion distances than Ge and Si adatoms. Exchange between C adatoms and substrate atoms are obvious and the epitaxial thickness is small. Total potential energies of adatoms and substrate atoms involved in the simulation cell are computed. When a newly arrived adatom reaches the stable position, the potential energy of the system will decrease and the curves turns into a ladder-like shape. It is found that C adatoms can lead to more reduction of the system energy and the potential energy of the system will increase as temperature increases.

Investigation of the structural and dynamic basis of kinesin dissociation from microtubule by atomistic molecular dynamics simulations

Kinesin is a molecular motor that can step processively on microtubules via the hydrolysis of ATP molecules.An important factor characterizing the processivity of the kinesin motor is its dissociation from the microtubule.Here,using all-atom molecular dynamics simulations,we studied the dissociation process of the kinesin head in weak-microtubulebinding or ADP state from tubulin on the basis of the available high-resolution structural data for the head and tubulin.By analyzing the simulated snapshots of the structure of the head-tubulin complex we provided detailed structural and dynamic information for the dissociation process.We found that the dissociation of the head along different directions relative to the tubulin exhibits very different dynamic behaviors.Moreover,the potential forms or energy landscapes of the interaction between the head and tubulin along different directions were determined.The studies have important implications for the detailed molecular mechanism of the dissociation of the kinesin motor and thus are critical to the mechanism of its processivity.

Damage of low-energy ion irradiation on copper nanowire:molecular dynamics simulation

Physical and chemical phenomena of low-energy ion irradiation on solid surfaces have been studied systematically for many years, due to the wide applications in surface modification, ion implantation and thin-film growth. Recently the bombardment of nano-scale materials with low-energy ions gained much attention. Comared to bulk materials, nano-scale materials show different physical and chemical properties. In this article, we employed molecular dynamics simulations to study the damage caused by low-energy ion irradiation on copper nanowires. By simulating the ion bombardment of 5 different incident energies, namely, 1 keV, 2 keV, 3 keV, 4 keV and 5 keV, we found that the sputtering yield of the incident ion is linearly proportional to the energies of incident ions. Low-energy impacts mainly induce surface damage to the nanowires, and only a few bulk defects were observed. Surface vacancies and adatoms accumulated to form defect clusters on the surface, and their distribution are related to the type of crystal plane, e.g. surface vacancies prefer to stay on （100） plane, while adatoms prefer （110） plane. These results reveal that the size effect will influence the interaction between low-energy ion and nanowire.

Molecular Dynamics Study on Configuration Energy and Radial Distribution Functions of Ammonium Dihydrogen Phosphates Solution

Molecular dynamics simulations were carried out to study the configuration energy and radial distribution functions of mmonium dihydrogen phosphate solution at different temperatures. The dihydrogen phosphate ion was treated as a seven-site model and the ammonium ion was regarded as a five-site model, while a simple-point-charge model for water molecule. An unusually local particle number density fluctuation was observed in the system at saturation temperature. It can be found that the potential energy increases slowly with the temperature from 373 K to 404 K, which indicates that the ammonium dihydrogen phosphate has partly decomposed. The radial distribution function between the hydrogen atom of ammonium cation and the oxygen atom of dihydrogen phosphate ion at three different temperatures shows obvious difference, which indicates that the average H-bond number changes obviously with the temperature. The temperature has an influence on the combination between hydrogen atoms and phosphorus atoms of dihydrogen phosphate ion and there are much more growth units at saturated solutions.

Molecular Dynamics Simulation of Interface Properties between Water-Based Inorganic Zinc Silicate Coating Modified by Organosilicone and Iron Substrate

The interface properties of Fe(101)/zinc silicate modified by organo-siloxane(KH-570)was studied by using the method of molecular dynamics simulation.By calculating the temperature and energy fluctuation of equilibrium state,equilibrium concentration distribution,MSD of layer and different groups,and interaction energy of two interface models,the influencing mechanism on the interface properties of adding organosiloxane into coating system was studied at the atomic scale.It shows that the temperature and energy of interface oscillated in a small range and it was exited in a state of dynamic equilibrium within the initial simulation stage(t<20 ps).It can be seen from the multiple peak states of concentration distribution that the iron substrate,organo-siloxane and zinc silicate are distributed in the form of a concentration gradient in the real environment.The rapid diffusion of free zinc powder in zinc silicate coating was the essential reason that affected the comprehensive properties of coating.The interface thickness decreased from 7.45 to 6.82Å,the MSD of free zinc powder was effectively reduced,and the interfacial energy was increased from 104.667 to 347.158 kcal/mol after being modified by organo-siloxane.

Inhibition Mechanism of Hydroxyproline-like Small Inhibitors to Disorder HIF-VHL Interaction by Molecular Dynamic Simulations and Binding Free Energy Calculations

Protein-protein interactions are vital for a wide range of biological processes.The interactions between the hypoxia-inducible factor and von Hippel Lindau(VHL)are attractive drug targets for ischemic heart disease.In order to disrupt this interaction,the strategy to target VHL binding site using a hydroxyproline-like(pro-like)small molecule has been reported.In this study,we focused on the inhibition mechanism between the pro-like inhibitors and the VHL protein,which were investigated via molecular dynamics simulations and binding free energy calculations.It was found that pro-like inhibitors showed a strong binding affinity toward VHL.Binding free energy calculations and free energy decompositions suggested that the modification of various regions of pro-like inhibitors may provide useful information for future drug design.

Molecular dynamics simulations in hydrogel research and its applications in energy utilization: A review

Hydrogels are soft,highly absorbent and water-retaining polymers that are widely used in energy utilization.Molecular dynamics(MD)simulation is powerful in exploring micro/nano mechanisms and can assist material regulation and experimental design.This review summarizes recent MD simulations on the composition and structure characteristics of physically and chemically crosslinked hydrogels,focusing on the functionalities such as mechanical properties,heat transfer performance,hygroscopic properties and photocatalytic applications required in the energy conversion process.The fundamentals of MD simulations are also introduced,along with common modeling procedures for hydrogels.Literature review showed that MD simulations can visually display molecular-scale changes during cross-linking and absorption processes,thereby predicting changes in intermolecular interactions and associated microstructural change.Challenges for future research include constructing hydrogel networks that can be experimentally verified,and developing appropriate molecular force fields under various operating conditions.Incorporating quantum mechanics or coarse-graining methods in MD simulations further broaden its application into electronic or mesoscopic problems.Combining with machine learning,finite element or lattice Boltzmann methods may be also promising as it can be used to reveal the influence of 3D pores within hydrogels.This study aims to promote the use of MD simulations in exploring characteristics and mechanisms of hydrogel and other polymer materials in energy utilization.

Morphology prediction of dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) crystal in different solvent systems using modified attachment energy model

In order to theoretically study the growth morphology of dihydroxylammonium 5,5’-bistetrazole-1,1’-dio late(TKX-50)crystal in different solvent systems,crystal–solvent models were established,and then molecular dynamics(MD)methods were adopted as a means to simulate particle motion.Modified attachment energy(MAE)model was employed to calculate the growth morphology of TKX-50.The simulation results demonstrate that COMPASS force field and RESP charge are suitable for molecular dynamics simulation of TKX-50.The morphologically dominant growth surfaces of TKX-50 in vacuum are(020),(011),(11–1),(100)and(120),respectively.In water(H_(2)O)and N,N-dimethylformamide(DMF)solvents,the(11–1)face is the largest in the habit face,the growth rate of(020)face becomes faster.With the increase of temperature,the aspect ratios of TKX-50 crystal in DMF solvent increase,and the areas of the(120)faces decrease.In ethylene glycol/H_(2)O mixed solvent system with volume ratio of 1/1,aspect ratio of TKX-50 is relatively small.In formic acid/H_(2)O mixed solvents with different volume ratios(1/4,1/3,1/2,1/1 and 2/1),aspect ratio of TKX-50 is relatively small when volume ratio is 1/2.

Using thermodynamic parameters to study self-healing and interface properties of crumb rubber modified asphalt based on molecular dynamics simulation

The thermodynamic property of asphalt binder is changed by the addition of crumb rubber,which in turn influences the self-healing property as well as the cohesion and adhesion within the asphalt-aggregate system.This study investigated the self-healing and interface properties of crumb rubber modified asphalt(CRMA)using thermodynamic parameters based on the molecular simulation approach.The molecular models of CRMA were built with representative structures of the virgin asphalt and the crumb rubber.The aggregate was represented by SiO2 and Al2O3 crystals.The selfhealing capability was evaluated with the thermodynamic parameter wetting time,work of cohesion and diffusivity.The interface properties were evaluated by characterizing the adhesion capability,the debonding potential and the moisture susceptibility of the asphalt-aggregate interface.The self-healing capability of CRMA is found to decrease as the rubber content increases.The asphalt-Al2O3 interface with higher rubber content has stronger adhesion and moisture stability.But the influence of crumb rubber on the interfacial properties of asphalt-SiO2 interface has no statistical significance.Comparing with the interfacial properties of the asphalt-SiO2 interface,the asphalt-Al2O3 interface is found to have a stronger adhesion but a worse moisture susceptibility for its enormous thermodynamic potential for water to displace the asphalt binder.

Swelling of K＋, Na＋ and Ca2＋-montmorillonites and hydration of interlayer cations： a molecular dynamics simulation

This paper performs molecular dynamics simulations to investigate the role of the monovalent cations K, Na and the divalent cation Ca on the stability and swelling of montmorillonite. The recently developed CLAYFF force field is used to predict the basal spacing as a function of the water content in the interlayer. The simulations reproduced the swelling pattern of these montmorillonites, suggesting a mechanism of their hydration different （K＋ 〈 Na＋ 〈 Ca2＋） from that of K＋-, Na＋-, and Ca2＋-montmorillonites. In particular, these results indicate that the valence of the cations has the larger impact on the behaviour of clay water systems. It also finds that the differences in size and hydration energy of K＋, Na＋ and Ca2＋ ions have strong implications for the structure of interlayer. This leads to the differences in the layer spacings of the simulated K＋-, Na＋-, and Ca2＋-montmorillonites. Furthermore, these simulations show that the K cations interact strongly with the clay sheets for the dehydrated clay sheets, but for the hydrated clays the Ca cations interact clearly strongly with the clay sheets.

Free energy calculation of single molecular interaction using Jarzynski's identity method:the case of HIV-1 protease inhibitor system

Jarzynski＇ identity （JI） method was suggested a promising tool for reconstructing free energy landscape of biomolecular interactions in numerical simulations and ex- periments. However, JI method has not yet been well tested in complex systems such as ligand-receptor molecular pairs. In this paper, we applied a huge number of steered molec- ular dynamics （SMD） simulations to dissociate the protease of human immunodeficiency type I virus （HIV-1 protease） and its inhibitors. We showed that because of intrinsic com- plexity of the ligand-receptor system, the energy barrier pre- dicted by JI method at high pulling rates is much higher than experimental results. However, with a slower pulling rate and fewer switch times of simulations, the predictions of JI method can approach to the experiments. These results sug- gested that the JI method is more appropriate for reconstruct- ing free energy landscape using the data taken from experi- ments, since the pulling rates used in experiments are often much slower than those in SMD simulations. Furthermore, we showed that a higher loading stiffness can produce higher precision of calculation of energy landscape because it yields a lower mean value and narrower bandwidth of work distri- bution in SMD simulations.

Etching Mechanisms of CF_3 Etching Fluorinated Si:Molecular Dynamics Simulation

Molecular dynamics simulations are performed to investigate CF3 continuously bom- barding the amorphous silicon surface with energies of 10 eV, 50 eV, 100 eV and 150 eV at normal incidence and room temperature. The improved Tersoff-Brenner potentials were used. The simulation results show that the steady-state etching rates are about 0.019, 0.085 and 0.1701 for 50 eV, 100 eV and 150 eV, respectively. With increasing incident energy, a transition from C-rich surface to F-rich surface is observed. In the region modified by CF3, SiF and CF species are dominant.

Measuring the Spontaneous Curvature of Bilayer Membranes by Molecular Dynamics Simulations

We propose a mathematically rigorous method to measure the spontaneous curvature of a bilayer membrane by molecular dynamics(MD)simulation,which provides description of the molecular mechanisms that cause the spontaneous curvature.As a main result,for the membrane setup investigated,the spontaneous curvature is proved to be a constant plus twice the mean curvature of the membrane in its tensionless ground state.The spontaneous curvature due to the built-in transbilayer asymmetry of the membrane in terms of lipid shape is studied by the proposed method.A linear dependence of the spontaneous curvature with respect to the head-bead diameter difference and the lipid mixing ratio is discovered.The consistency with the theoretical results provides evidence supporting the validity of our method.

Molecular Dynamic Simulation of Melting Points of Trans-1,4,5,8- tetranitro-1,4,5,8-tetraazadacalin （TNAD） with Some Propellants

Molecular dynamic simulation was employed to predict the melting points Tm of TNAD/HMX, TNAD/RDX, TNAD/DINA, and TNAD/DNP systems （tans-1,4,5,8- tetranitro-1,4,5,8-tetraazadacalin （TNAD）, dinitropiperazine （DNP）, cyclotetramethylenetetranitroamine （HMX）, cyclotrimethylenetrinitramine （RDX）, and N-nitrodihydroxyethylaminedinitrate （DINA））. Tm was determined from the inflexion point on the curve of mean specific volume vs. temperature. The result shows that the Tm values of TNAD/HMX, TNAD/RDX, and TNAD/DINA systems are 500, 536, and 488 K, respectively. The TNAD/DNP system has no obvious Tm value, which shows the system is insoluble. Using Tm, the solubility of the four systems was analyzed. The radial distribution functions of the four systems were analyzed and the main intermolecular forces between TNAD and other energetic components are short-range interactions. The better the solubility is, the stronger the intermoleenlar interaction is. In addition, the force field energy at different temperature was also analyzed to predict Tm of the four systems.

Hydrogen Diffusion in Aluminum Melts: An ab initio Molecular Dynamics Study

The diffusion process of hydrogen in aluminum melts was investigated by molecular dynamics simulation. The pair correlation function, first peak position, and coordination number was calculated and differences in the structural properties among Al-H, Cl-H, and Al-Cl pair were examined. The mechanism of chlorine on improving hydrogen diffusion was discussed. From an ab initio molecular dynamics calculations, the diffusivity of hydrogen in liquid aluminum as D（T）=（0.118×10-4 m2/s）exp（-0.316 eV/kT） is obtained, which is in good agreement with the experimental data. Correspondingly the diffusivity with presence of chlorine is promoted as D（T）=（0.09×10-4 m2/s）exp（-0.251 eV/kT）. It can be concluded that the diffusion of hydrogen in aluminum melts can be enhanced in the presence of chlorine.