Narrow Results

The phase transition of metals is a research hotspot in molecular dynamic (MD) simulation. With the increase of the development of MD, different force fields with different requirements have emerged, which helps to select the appropriate force field and also increases the difficulty of selection. In addition, previous studies have been affected by particle size, which affects the melting point accuracy. MD simulation of the melting and condensing behavior of Aluminum (Al) particles was carried out by using EAM force fields from different sources. The thermal behavior of phase transition was studied by means of potential energy, specific heat, MSD, FCC lattice number, etc. The melting and condensation process of 2–10nm cubic without boundary under the NPT system was simulated, and the steady-state simulation was discussed by means of an isometric temperature point. It is proved that the borderless simulation can completely eliminate the boundary effect. The parameter setting of efficient use of EAM is widely discussed by using this method, and the effectiveness of the EAM force field is compared, so as to improve the efficiency of scholars engaged in related research and avoid the difficult choice of force field files. The results show that the borderless simulation has quite high advantages in terms of phase transition potential energy and melting point, while the current EAM force field is inherently deficient in this kind of discussion, and the development of new force field is urgent.

We show that the dramatic dependence of pressure on the parameters of the inter-molecular potential can be exploited to tune them to their best values. We support the viability of this strategy by a careful study of a fully diffusive Lennard–Jones fluid, showing that Lennard–Jones parameters can be easily optimized to better than a 1% accuracy.

The heat transfer and oxygen transport behaviors of Ti-6Al and Fe-12Cr alloys directly affect their aeronautical material application. In order to investigate the flame retardant mechanism in atomic scale, molecular dynamic (MD) simulations were performed to study the heat transfer and oxygen transport performances of Ti-6Al and Fe-12Cr alloys in the linear and uniform heating treatment. Next, the ignition performances of Ti-6Al and Fe-12Cr alloys were further verified by the frictional ignition tests. Therefore, this is a multi-scale research with a novel combination of MD simulations and ignition tests. Those obtained results show that the heat is more concentrated at the heating edge of Ti-6Al alloy while at the same heating rate. This leads to the intensification of atomic motion at the heating edge, and reduces the structural thermal stability of Ti-6Al alloy’s heating edge. Therefore, the heat transfer performance of Fe-12Cr alloy at the same state is better than that of Ti-6Al alloy. When there is an oxide layer on the surface of these two alloys, Fe-12Cr alloy can inhibit the oxygen transfer more effectively than Ti-6Al alloy, and further improve its flame retardant property. In addition, the frictional ignition tests with Ti alloy rotor under the same airflow environment show that the critical airflow velocity of the Fe-12Cr alloy stator is about 114m/s higher than that of Ti-6Al-4V alloy stator at 384^∘. Generally, according to MD simulations and frictional ignition tests, it could be concluded that the flame retardancy of Fe-12Cr alloy is higher than Ti-6Al alloy.

We present a framework to design force fields that drive particles to follow a path under the physics-based animation system. In this framework, a user interactively specifies the desired path, represented by a Bezier curve using a GUI and the attraction force that drives a particle toward the target location. Then, the framework automatically defines the steering force to make a particle follow the desired path. To this end, we use B-splines to define the steering force that best approximates the user-specified path. We demonstrate the effectiveness of our method by showing a large number of particles following the desired path and forming an animated human figure. Our method creates a stable behavior of particles and is fast enough to run in real time.

In the present work, we have investigated solvent effects on the relative energies and dipole moment values and studied the structural properties of water, methanol, and ethanol surrounding single-walled carbon nanotube (SWCNT) and mixtures of them as well, using Molecular Dynamics simulation. Because some of the physicochemical parameters are related to structural properties of SWCNT, we used different force fields to determine energy and other types of geometrical parameters, on the particular SWCNT. Because of the differences among force fields, the energy of a molecule calculated using two different force fields will not be the same. In this study, the difference in the force fields is illustrated by comparing the calculated energies by using force fields such as MM+, AMBER, and BIO+. The Quantum Mechanics (QM) calculations were carried out with the GAUSSIAN 98 program based on HF/3-21G level. In this study, we have compared gas phase and solvent calculations that considered solvents such as water, methanol, ethanol, and mixtures of them. So, in this work, we investigated polar solvents effects on SWCNT within the Onsager self-consistent reaction field (SCRF) model using a Hartree–Fock method and the temperature effect on the stability of SWCNT in various solvents.

Artemisinin is widely employed to treat malaria. A variety of experiments have been done to research the dissolution property of artemisinin in different solvents. To have an in-depth understanding of the property, it is essential to explore the dissolution property from molecular level with molecular dynamics (MD) simulation, which needs a satisfactory force field of artemisinin. Therefore in the research a quantum chemistry based force field was developed. The quantum chemical calculation at different levels was done and Hartree–Fock (HF) level calculation gives satisfactory results. The charge distribution was then determined successfully. The van der Waals (VDW) parameters of the C unit with sp³-C were tuned according to the difference between the dissolution enthalpy of artemisinin in ethanol and ethyl acetate. With the developed force field, MD method was employed to successfully simulate the dissolution property of artemisinin in different solvents. The simulation results show that artemisinin molecules tends to aggregate in water, while in the aqueous solution of ethanol, the same number of artemisinin molecules tends to disperse. Furthermore, simulation results show that 8 M ethyl acetate aqueous solution has better dissolution ability than 8 M ethanol aqueous. The simulation gave agreements with the experimental results.

In this paper, molecular dynamics (MD) simulations were performed for a number of benchmark proteins using both the standard assisted model building with energy refinement (AMBER) charge and the dynamically adjusted polarized protein-specific charge (DPPC) from quantum fragment calculations to provide accurate electrostatic interactions. Our result shows that proteins' dynamic structures drifted away from the native structures in simulations under standard (nonpolarizable) AMBER force field. For comparison, proteins' native structures were dynamically stable after a long time simulation under DPPC. The free energy landscape reveals that the native structure is the lowest energy conformation under DPPC, while it is not under standard AMBER charge. To further investigate the polarization effect on the stability of native structures of proteins, we restarted from some decoy structures generated from simulations using standard AMBER charges and then carried out further MD simulation using DPPC to refine those structures. Our study shows that the native structures from these decoy structures can be mostly recovered using DPPC and that the dynamic structures with the highest population in cluster analysis are in close agreement with the corresponding native structures. The current study demonstrates the importance of electronic polarization of protein in stabilizing the native structure.

Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three AMBER force fields ff99, ff99SB, and ff03. The generalized order parameters for amide backbone are calculated from the three force fields and compared with the NMR S2 values. We found that the ff99SB and ff03 force field calculated order parameters agree reasonably well with the NMR S2 values, whereas ff99 calculated values deviate most from the NMR order parameters. Stereochemical geometry of protein models from each force field also agrees well with the remarks from NMR S2 values. However, between ff99SB and ff03, there are several differences, most notably in the loop regions. It is found that these loops are, in general, more flexible in the ff03 force field. This results in a larger active site cavity in the simulation with the ff03 force field. The effect of this difference in computer-aided drug design against flexible receptors is discussed.

In this study, we firstly characterize modified magnetic particles and associated magnetic fields by considering the evolution of the charged particle together with its modified frame construction in 3D space. Then, we compute the energy flows of each modified magnetic particles in terms of its curvature and torsion in the space. Finally, we obtain energy flux density, the intensity of the light, power of modified magnetic particles in the space.

In the present paper, we propose a heuristic and intuitive approach to visualize how force fields “move” when their source moves at a constant velocity $v$ or accelerates with acceleration $a$ relative to a stationary observer. Our approach is based on the application of the principle of relativity and the principle of equivalence and holds regardless of the nature of the force field. The results presented here have been derived in the nonrelativistic approximation ($v\ll c$ and $a\mathrm{\Delta }t\ll c$, $\mathrm{\Delta }t$ being the interval of time within which we observe the field). We shall show that in both cases of uniform and accelerated motion of the source, the field moves rigidly with the source. Namely, for every observer, however distant from the source, the field is always directed away from (or points towards) the present, instantaneous position of the source. We also show that these results are in agreement with what we know from experimental evidence and full-fledged physical theories (of electromagnetism and gravitation) beyond the nonrelativistic approximation. The proposed approach may be considered as a tool to facilitate students in graduate and undergraduate courses to familiarize themselves with (and self convince of) such a counter-intuitive feature of the force fields.

Bonded (or valence) interactions, which directly determine the local structures of the molecules, are fundamental parts of molecular mechanics force fields (FFs). Most popular classical FFs adopt the simple harmonic models for bond stretching and angle bending and ignore cross-coupling effects among the valence terms. This may lead to less accurate vibrational properties and configurations in molecular dynamics (MD) simulations. AMOEBA models utilize an MM3(MM4)-style bonded interaction model, in which the vibrational anharmonicity, the coupling effects among different energy terms, and the out-of-plane bending for sp2-hybridized atoms are considered. In this work, we report the development of bonded interaction parameters for a wide range of chemistry based on quantum mechanics (QM). About 270 atomic types defined by SMARTS strings were used to model the valence interactions. Our results indicate that the resulting valence parameters produce accurate vibrational frequencies (RMSD from QM is less than ∼36.6cm⁻¹) over a large set of molecules with diverse functional groups (445 molecules). By contrast, the harmonic models usually give an RMS error greater than 60cm⁻¹. Meanwhile, this model accurately reflects the potential energy surface of the out-of-plane bending. Our model can generally be applied to the AMOEBA family and any MM3(MM4)-based molecular mechanics FFs.

Bonded (or valence) interactions, which directly determine the local structures of the molecules, are fundamental parts of molecular mechanics force fields (FFs). Most popular classical FFs adopt the simple harmonic models for bond stretching and angle bending and ignore cross-coupling effects among the valence terms. This may lead to less accurate vibrational properties and configurations in molecular dynamics (MD) simulations. AMOEBA models utilize an MM3(MM4)-style bonded interaction model, in which the vibrational anharmonicity, the coupling effects among different energy terms, and the out-of-plane bending for sp2-hybridized atoms are considered. In this work, we report the development of bonded interaction parameters for a wide range of chemistry based on quantum mechanics (QM). About 270 atomic types defined by SMARTS strings were used to model the valence interactions. Our results indicate that the resulting valence parameters produce accurate vibrational frequencies (RMSD from QM is less than ∼ 36:6 cm⁻¹) over a large set of molecules with diverse functional groups (445 molecules). By contrast, the harmonic models usually give an RMS error greater than 60 cm⁻¹. Meanwhile, this model accurately reflects the potential energy surface of the out-of-plane bending. Our model can generally be applied to the AMOEBA family and any MM3 (MM4)-based molecular mechanics FFs.