All-Atom Direct Folding Simulation for Proteins Using the Accelerated Molecular Dynamics in Implicit Solvent Model

We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.

A possible probe to neutron-skin thickness by fragment parallel momentum distribution in projectile fragmentation reactions

Neutron-skin thickness is a key parameter for a neutron-rich nucleus;however,it is difficult to determine.In the framework of the Lanzhou Quantum Molecular Dynamics(LQMD)model,a possible probe for the neutron-skin thickness(δ_(np))of neutron-rich ^(48)Ca was studied in the 140A MeV ^(48)Ca+^(9)Be projectile fragmentation reaction based on the parallel momentum distribution(p∥)of the residual fragments.A Fermi-type density distribution was employed to initiate the neutron density distributions in the LQMD simulations.A combined Gaussian function with different width parameters for the left side(Γ_(L))and the right side(Γ_(R))in the distribution was used to describe the p∥of the residual fragments.Taking neutron-rich sulfur isotopes as examples,Γ_(L) shows a sensitive correlation withδ_(np) of ^(48)Ca,and is proposed as a probe for determining the neutron skin thickness of the projectile nucleus.

U-model Enhanced Dynamic Control of a Heavy Oil Pyrolysis/Cracking Furnace

This paper proposes a case study in the control of a heavy oil pyrolysis/cracking furnace with a newly extended U-model based pole placement controller(U-PPC). The major work of the paper includes: 1) establishing a control oriented nonlinear dynamic model with Naphtha cracking and thermal dynamics; 2) analysing a U-model(i.e., control oriented prototype) representation of various popular process model sets; 3)designing the new U-PPC to enhance the control performance in pole placement and stabilisation; 4) taking computational bench tests to demonstrate the control system design and performance with a user-friendly step by step procedure.

Progress of quantum molecular dynamics model and its applications in heavy ion collisions

In this review article,we first briefty introduce the transport theory and quantum molecular dynamics model applied in the study of the heavy ion collisions from low to intermediate energies.The developments of improved quantum molecular dynamics model(ImQMD)and ultra-relativistic quantum molecular dynamics model(UrQMD),are reviewed.The reaction mechanism and phenomena related to the fusion,multinucleon transrer,fragmentation,collective flow and particle production are reviewed and discussed within the framework of the two models.The constraints on the isospin asymmetric muclear equation of state and in-medium nucleon nucleon cross sections by comparing the heavy ion collision data with transport models calculations in last decades are also discussed,and the uncertainties of these constraints are analyzed as well.Finally,we discuss the future direction of the development of the transport models for improving the understanding of the reaction mechanism,the descriptions of various observables,the constraint on the nuclear equation of state,as well as for the constraint on in-medium nucleon-nucleon cross sections.

Numerical simulation of two-dimensional granular shearing flows and the friction force of a moving slab on the granular media

This paper studies some interesting features of two-dimensional granular shearing flow by using molecular dynamic approach for a specific granular system. The obtained results show that the probability distribution function of velocities of particles is Gaussian at the central part, but diverts from Gaussian distribution nearby the wall. The macroscopic stress along the vertical direction has large fluctuation around a constant value, the non-zero average velocity occurs mainly near the moving wall, which forms a shearing zone.. In the shearing movement, the volume of the granular material behaves in a random manner. The equivalent fl＇iction coefficient between moving slab and granular material correlates with the moving speed at low velocity, and approaches constant as the velocity is large enough.

Secondary decay effects of the isospin fractionation in the projectile fragmentation at GeV/nucleon

The isospin fractionations in 124Sn,107Sn+120Sn at 600 MeV/nucleon,and 136Xe,124Xe+208Pb at 1000 MeV/nucleon are investigated by the isospin-dependent quantum molecular dynamics model coupled with the statistical code GEMINI.The yield ratio as a function of the binding energy difference for light mirror nuclei 3H/3He,7Li/7Be,11B/11C,and 15N/15O is applied to estimate the ratio between neutrons and protons in the gas of the fragmenting system.By comparing the estimated values resulting from the simulations with and without the GEMINI code,it was found that the secondary decay distorts the signal of the isospin fractionation.To minimize the secondary decay effects,the yield ratio of the light mirror nuclei 3H/3He as well as its double ratio between two systems with different isospin asymmetries of the projectiles is recommended as robust isospin observables.

Atomistic Simulations of the Mechanical Deformation of Irradiation-amorphized Silicon Carbide

Irradiation-induced atomic-scale defects and lattice disorder in Silicon Carbide （SIC） can significantly affect the material＇s mechanical properties. Currently there lacks a unified physical model capable of describing the law in which the properties of SiC scale with the accumulation of defects, especially in terms of the underlying physical mechanism. To develop fundamental models that are capable of describing the various physical properties of SiC as a function of microstructural change, molecular dynamics simulations of uniaxial tension were performed on a series of irradiation-amorphized SiC （a-SiC） samples with a range of imposed chemical disorder, which is defined as the ratio between the number of homonuclear bonds and heteronuclear bonds （x = Nc-c / Nsi-c）. With increasing chemical disorder, significant alternation of mechanical response of a-SiC has been detected in terms of increasingly pronounced plastic flow. Meanwhile relevant mechanical properties, including Young＇s modulus, strength, yield stress and strain, as well as failure strain scale monotonically with chemical disorder while in distinct manners. Specifically slight chemical disorder （x = 0.045） could induce substantial reduction of Young＇s modulus up to -2%, whereas strength basically linearly varies with chemical disorder until x≈0.5 upon which the variations in mechanical properties tend to saturate. Further examination of the evolution of atomic structure of a-SiC reveals a crossover of deformation mechanisms from homogeneous elastic deformation to localized plastic flow, which accounts for the strong chemical disorder dependence of the mechanical properties as well as mechanical responses of amorphous SiC. This crossover is also manifested in switching of fracture mode from brittle failure dominated by lattice instability in the ligaments between topological disordered clusters to nanoductile failure preceded by percolation of nanocavities. Employing chemical disorder to measure the defect concentration of a-SiC could contribute to the quantification of the correlation between mechanical properties and the corresponding defective a-SiC structure. Moreover the distinct scale laws shown by Young＇s modulus and strength with chemical disorder and the proposed critical chemical disorder threshold could benefit the quantitative evaluations of the mechanical performances of SiC components in different irradiation environments.

Modeling the epidemic dynamics of COVID-19: Agent-based approach including molecular dynamics simulation and SEIR type methods

In this study, we developed a SEIR model, including social interactions and individualhuman mobility in everyday activities. For this purpose, daily mobility of people wasconsidered by using the molecular dynamic method and the virus spreading was modeledemploying the ordinary SEIR scheme. Utilizing this model, the variation of populationsize, density, and health strategy as well as the effect of busy places such as malls,were considered. The results show that our flexible model is able to consider the effectsof different parameters such as distance between peoples, local population density andhealth strategy in the outbreak.

Nuclear dynamical octupole deformation in heavy-ion reactions

Within the quantum molecular dynamics （QMD） model, the dynamical octupole deformation is studied as a function of the central distance between the projectile and target in the approaching process of heavy-ion fusion reactions. The dependence of the maximum dynamical octupole defor- mations on tile incident energies is also investigated. The dynamical octupole deformations can be observed during the approaching process, and the maximum dynamical octupole deformations be- come more significant with decreasing incident energies. The distributions of the proton and neutron centers in the projectile and target are also investigated, respectively. In the approaching process of heavy-ion fusion reactions, the separation between proton centers for two nuclei is larger than that between neutron centers because of the strong Coulomb potential.

Statistical properties of pseudo-particle systems

Pseudo-particle modeling （PPM）, a molecular modeling method which combines time-driven algorithms and hard molecule modeling, was originally developed for simulating gas in complex multiphase systems （Ge ＆ Li, 2003; Ge et al., 2005; Ge, 1998）. In this work, the properties of two- and three-dimensional pseudo-particle systems, namely, mean free path, compressibility factor, self-diffusion coefficient and shear viscosity, are systematically measured by using PPM. it is found that in terms of an effective diameter, the results well conform to the Chapman-Enskog theory, thus suggesting that PPM can be employed to simulate the micro- and meso-scale behavior of ordinary gas and fluid flows.

Modeling nanoscale ice adhesion

Anti-icing is crucial for numerous instruments and devices in low temperature circum- stance. One of the approaches in anti-icing is to reduce ice adhesion strength, seeking spontaneous de-icing processes by natural forces of gravity or by winds. In order to enable tai- lored surface icephobicity design, research requires a good theoretical understanding of the atomistic interacting mechanisms between water/ice molecules and their adhering substrates. Herein, this work focuses on using atomistic modeling and molecular dynamics simulation to build a nanosized ice-cube adhering onto silicon surface, with different contact modes of solid-solid and solid-liquid-solid patterns. This study provides atomistic models for probing nanoscale ice adhesion mechanics and theoretical platforms for explaining experimental results.

Triaxial tension-induced damage behavior of nanocrystalline NiTi alloy and its dependence on grain size

This study focused on the effect of grain size(GS)on dynamic damage performance of nano-crystalline nickel titanium(NC NiTi)alloy.Molecular dynamics simulations were conducted to triaxially expand it at a high strain rate(4×10~9 s^(-1)),while the temperature and initial pressure remained 300 K and 0 bar,respectively.It was discovered that the superelastic NiTi alloy exhibited the similar damage response as ductile metallic materials,which was vividly characterized by void nucleation,growth,and coalescence.The stress-strain curves demonstrated that the void nucleations always occurred near the start of the strain softening region at various grain sizes.Interestingly,it was discovered that the void evolution was characteristic of an almost double-linear behavior,and the piecewise linearity became more prominent for the void volume fraction increase at larger grain size.More importantly,the fracture behavior was found to be strongly dependent upon the grain size in the NC NiTi alloy.For small grain size,the existing voids propagated along the grain boundaries and in the grains,leading to intergranular and transgranular fracture.Contrarily,the intergranular-dominated fracture was responsible for the void propagation in the large grain.In addition,the starting time,ending time,and threshold of void nucleation were found to be weak sensitivity to GS,and a reverse effect was appropriate to the void growth.The results highlighted that as the GS increased,more complete stress relaxation and shorter duration time were produced,leading to larger void volume fraction and faster growth rate.

Probing the symmetry potential with neutron-proton bremsstrahlung in heavy-ion collisions

In the framework of the isospin-dependent quantum molecular dynamics transport model （QMD）, the effects of symmetry potential on the collision number and the neutron-proton bremsstrahlung photon in the reactions of 40Ca＋40Ca, 124Sn＋124Sn, 40Ca＋64Zn, 40Ca＋124Sn at different incident beam energies are studied. It is found that the collision number shows moderate sensitivity to the stiffness of the symmetry potential and the number of hard photons calculated with stiff symmetry potential is obviously smaller than that with soft symmetry potential. Thus, the neutron-proton bremsstrahlung photons produced in heavy-ion collisions may be a useful probe for the high-density behavior of the nuclear symmetry potential.

Theoretical uncertainties on the extraction of in-medium NN cross sections by different Pauli blocking algorithms

Three typical Pauli blocking algorithms in quantum molecular dynamics type models are investigated in the nuclear matter,the nucleus,and heavy ion collisions.In nuclear matter,the blocking ratios obtained with the three algorithms are underestimated by 13%-25%compared to the corresponding analytical values.For a finite nucleus,spurious collisions occur around the surface of the nucleus owing to the defects of the Pauli blocking algorithms.In the simulations of heavy ion collisions,the uncertainty of stopping power arising from the different Pauli blocking algorithms is less than 5%.Furthermore,the in-medium effects of nucleon-nucleon(NN)cross sections on the nuclear stopping power are discussed.Our results show that the transport model calculations with free NN cross sections result in the stopping power decreasing with beam energy when the beam energy is less than 300 MeV/u.To increase or decrease the values of the stopping power,the transport model calculations need enhanced or suppressed model dependent in-medium NN cross sections that are expected to be smaller than the true in-medium NN cross sections.

Orientation dichroism effect of proton scattering on deformed nuclei

Proton-induced scattering of 238U nuclei,with spheroidal deformations at beam energies above 100 MeV,is simulated using an improved quantum molecular dynamics model.The angular distribution of the deflected protons is highly sensitive to the orientation of the symmetrical long axis of the target nuclei with respect to the beam direction.As a result,in reverse kinematic reactions,an orientation dichroism effect is predicted,implying that the absorption rate of the 238U beam by a proton target discerns between the parallel and perpendicular orientations of the deformed 238U nuclei.