Article
Chemistry, Physical
Stefanie Kieninger, Bettina G. Keller
Summary: This study shows that the GROMACS Stochastic Dynamics (GSD) integrator is equivalent to the less frequently used splitting method BAOA in molecular dynamics simulations. It indicates that GSD and BAOAB generate the same configurations with high configurational accuracy, but GSD/BAOA has higher kinetic accuracy than BAOAB.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Jiuyang Liang, Pan Tan, Liang Hong, Shi Jin, Zhenli Xu, Lei Li
Summary: We have developed a new RBE method for molecular dynamics simulations of charged particles in a periodic box. This method is accurate, highly efficient, and scalable, allowing for efficient computation in large-scale systems and achieving satisfactory results.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biology
Sean T. Smrt, Cristian A. Escobar, Souvik Dey, Timothy A. Cross, Huan-Xiang Zhou
Summary: Mtb infects a quarter of the worldwide population and the rising drug resistance makes it urgent to better understand Mtb cell division. The study reveals that the transmembrane protein FtsQ may serve as a membrane anchor of the Mtb Z-ring, and its disordered cytoplasmic region interacts with multiple partners, indicating its potential role in cell division and as a drug target.
COMMUNICATIONS BIOLOGY
(2023)
Article
Computer Science, Interdisciplinary Applications
Baoxia Li, Yang Liu, Haoyu Qi, Hanyu Tang, Feng Huang
Summary: In this paper, the effects of temperature on the structure and dynamics of a binary complex plasma system are investigated through two-dimensional Langevin dynamics simulation. The results show that binary particles with different masses tend to distribute themselves separately with a boundary, which is more pronounced at lower temperatures. An optimum temperature is identified, which produces a separation distribution with the fewest small particles mixing in the region of large particles. The dynamical investigation reveals that small particles first reach the system center and are then pushed out by large particles. Overall, the structure and dynamics of the binary complex plasma are significantly influenced by the system temperature.
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Computer Science, Interdisciplinary Applications
Baoxia Li, Yang Liu, Xiaojiang Tang, Guannan Shi, Haoyu Qi, Xin Liu, Eric Robert, Feng Huang
Summary: In this paper, Langevin dynamics simulation is used to investigate the influence of particle number on the structures and dynamics of a binary complex plasma. The structures are characterized by particle distribution, nearest-neighbor, and pair correlation function, while the dynamics are characterized by the evolution of average speed, kinetic energy, mean square displacement (MSD), and self-diffusion coefficient. The study reveals that the structure and dynamics of the binary complex plasma are affected by the dust particle number.
COMPUTER PHYSICS COMMUNICATIONS
(2023)
Article
Chemistry, Multidisciplinary
Akito Kawai, Yoshihiro Kobashigawa, Kenshiro Hirata, Hiroshi Morioka, Shuhei Imoto, Koji Nishi, Victor Tuan Giam Chuang, Keishi Yamasaki, Masaki Otagiri
Summary: In this study, the relationship between the induced CD spectra and the structural features of the HSA complexes with ARP or deschloro-ARP was examined using several methods, including CD spectroscopic analysis, X-ray crystallographic analysis, and molecular dynamics simulations. The results showed that the induced CD spectra of the HSA complexes were influenced by temperature and that both ARP and deschloro-ARP were bound at the site II pocket in HSA, but with different molecular motions and interactions.
Article
Physics, Multidisciplinary
Meng Su, Davide Bernardi, Benjamin Lindner
Summary: A recent stochastic pursuit model investigates the movement of chasers towards a target undergoing pure Brownian diffusion. The addition of an escape term allows the target to detect and evade the approaching chasers, resulting in qualitatively different behaviors depending on the chase speed. When multiple chasers are present, the overall behavior resembles that of the original diffusion model due to compensating escape terms when the target is surrounded.
NEW JOURNAL OF PHYSICS
(2023)
Article
Physics, Multidisciplinary
Syed Yunus Ali, Nabadip Choudhury, Debasish Mondal
Summary: The continuous heating of the Earth's surface and aerosphere leads to global warming, which may increase the probability of abnormally large precipitation accumulation in rainfall events. Using a stochastic climate model, this study finds that implementing a permanent upper limit in column integrated water vapor or an asymmetric stochastic resetting can reduce the excessively high accumulation probability of such rainstorms. The presence of an optimal upper limit of column integrated water vapor in the atmosphere determines the decrease in heavy precipitation accumulation. Introducing an asymmetric stochastic resetting compensates for the energy cost and reduces the probability of targeted precipitation accumulation to the desired extent.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Article
Chemistry, Physical
Kai Kang, Khosrow Shakouri, Geert-Jan Kroes, Aart W. Kleyn, Jorg Meyer
Summary: The dynamics of N atom scattering from N-covered Ag(1 1 1) were analyzed using the GLO method with different mass values. Results showed that using nitrogen mass gives a trend closer to the experimental results for the dependence of the energy of the in-plane scattered atoms on the scattering angle, but worse agreement with experiment for the angular distribution of the in-plane scattered atoms.
Article
Chemistry, Multidisciplinary
Xueqiong Fu
Summary: The plastic deformation of Ni/Al2O3 interface systems under high strain rates was investigated using classical molecular dynamics method. Two types of interface structures were established to explore the dislocation nucleation and propagation mechanisms. The fracture behavior strongly depended on the interface structure, with Type II showing higher yield strength due to more stable Ni-O bonds. At high strain rates, the formation of Lomer-Cottrell locks and Shockley dislocations were suppressed. This study provides insights into the deformation mechanisms of Ni/Al2O3 interfaces at extreme conditions.
Article
Computer Science, Interdisciplinary Applications
Dong An, Sara Y. Cheng, Teresa Head-Gordon, Lin Lin, Jianfeng Lu
Summary: XLMD is a general method for molecular dynamics simulations using quantum and classical many-body potentials, with recent advancements such as introducing stochastic modification and studying convergence rates for Stochastic-XLMD. It has been shown to provide accurate dynamics independent of initial conditions, demonstrating effectiveness for water molecules described by a polarizable force field.
JOURNAL OF COMPUTATIONAL PHYSICS
(2021)
Article
Physics, Multidisciplinary
Dmitry Berkov, Elena K. Semenova, Natalia L. Gorn
Summary: The proposed algorithm allows for single-stage direct Langevin dynamics simulations over high energy barriers by introducing the concept of energy-dependent temperature. It enables more efficient computation of escape rates without increasing simulation time.
PHYSICAL REVIEW LETTERS
(2021)
Article
Physics, Condensed Matter
Ibrahim Buba Garba, Tommaso Morresi, Charles Bouillaguet, Michele Casula, Lorenzo Paulatto
Summary: We introduce a robust implementation of the temperature-dependent effective potential method in reciprocal space, which can be easily scaled to large cell and long sampling time. It is compatible with standard ab-initio molecular dynamics and Langevin dynamics. We demonstrate that efficient and accurate sampling can be achieved by using a thermostat to control temperature and dynamic parameters to optimize sampling efficiency. As an example, we use this method to investigate anharmonic phonon renormalization in weakly and strongly anharmonic materials, accurately reproducing the temperature effects on phonon frequencies, phase transition crossings, and stabilization of high-temperature phases.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2023)
Article
Materials Science, Multidisciplinary
Unal Domekeli
Summary: The study examined the effects of high pressure on the structural evolution of liquid metallic Ti62Cu38 alloy during rapid cooling. Results show that the pressure applied during rapid cooling strongly influences whether the alloy will transform into a crystal-like structure or a glassy structure. The study also found that the dominant clusters in the system shift from crystal-like clusters up to 10 GPa to icosahedral-like clusters at 10 GPa.
COMPUTATIONAL MATERIALS SCIENCE
(2021)
Article
Physics, Applied
Shruti Hariyani, Jakoah Brgoch, Florencio Garcia-Santamaria, Srinivas P. Sista, James E. Murphy, Anant A. Setlur
Summary: This article discusses the necessity of conducting downconverter reliability testing, as well as the potential for accelerating, screening, and understanding downconverter failure modes. The focus is on highlighting the mechanisms of failure, and how they influence materials selection and LED package design. The article also emphasizes the potential role of accelerated reliability testing protocols and first-principles calculations/data-driven models in establishing the compositional-processing trends for downconverter reliability. Possible research directions to improve downconverter reliability and the importance of assessing material stability are also highlighted.
JOURNAL OF APPLIED PHYSICS
(2022)