Refining potential energy surface through dynamical properties via differentiable molecular simulation by Bin Han, Kuang Yu

“…Abstract Recently, machine learning potential (MLP) largely enhances the reliability of molecular dynamics, but its accuracy is limited by the underlying ab initio methods. …”
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Mechanisms of wogonoside in the treatment of atherosclerosis based on network pharmacology, molecular docking, and experimental validation by Zhaohui Gong, Haixin Yang, Li Gao, Yi Liu, Qingmin Chu, Chuanjin Luo, Liang Kang, Huiqi Zhai, Qiang Xu, Wei Wu, Nan Li, Rong Li

“…Molecular docking and molecular dynamics simulations showed that wogonoside has good binding properties to the core targets. …”
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A Multiscale Model for Virus Capsid Dynamics by Changjun Chen, Rishu Saxena, Guo-Wei Wei

“…We show that the classical Navier-Stokes equation for the fluid dynamics and Newton's equation for the molecular dynamics can be derived from the least action principle. …”
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The Effects of Temperature and Impact Velocity on the Shock Wave Response of Pore-Embedded Metallic Glasses by Indrajit Patra, Ahmed M. Abdulhadi, Fatima Safaa Fahim, Bashar S. Bashar, Taif Alawsi, Mohammad Salmani

“…In this work, the shock wave response of a pore-embedded CuZr metallic glass (PEMG) under different impact velocities (0.5–1.5 km/s) and initial temperatures (300–600 K) was evaluated through the molecular dynamics (MD) simulation. The results indicated that the nucleation and growth of nanoscale shear events around the pore were the dominant mechanisms for plastic deformation under the shock wave. …”
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Structure Identification and Risk Assurance of Unknown Impurities in Pramipexole Oral Drug Formulation by Raymond R. Tjandrawinata, Antonius H. Cahyana, Ajeng O. Nugroho, Indra K. Adi, Joseph S. R. Talpaneni

“…Furthermore, observation of the binding affinity potential risk of these impurities to the pramipexole receptor has also been demonstrated through molecular docking and molecular dynamics simulation study. The binding energy result showed that pramipexole interaction with dopamine receptors D2 and D3 was higher than pramipexole mannose adduct and pramipexole ribose adduct.…”
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Discovery of ketene/acetyl as a potential receptor for hydrogen-transfer reactions in zeolites by Zhichao Guo, Qingteng Chen, Jian Liu, Bo Yang

“…Here, based on ab initio molecular dynamics simulations and free energy sampling methods, we discover a non-olefin-induced hydrogen-transfer reaction in the presence of CO, with ketene/acetyl emerging as a more suitable hydrogen-transfer receptor than olefins. …”
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Discovery of New Ligand with Quinoline Scaffold as Potent Allosteric Inhibitor of HIV-1 and Its Copper Complexes as a Powerful Catalyst for the Synthesis of Chiral Benzimidazole De... by Sabikeh G. Azimi, Ghodsieh Bagherzade, Mohammad Reza Saberi, Zeinab Amiri Tehranizadeh

“…The potency of these compounds as anti-HIV-1 agents was investigated using molecular docking into integrase (IN) enzyme with code 1QS4 and the GROMACS software for molecular dynamics simulation. The final steps were evaluated in case of RMSD, RMSF, and Rg. …”
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Effect of single particle potential on total cross section of nuclear reaction by Yan Fan, WenJun Guo, ZiHan Xi

“…In nuclear physics,the calculation of reaction cross-sections is an essential method for studying nuclear structure.By investigating the reaction cross-sections of different elements colliding with 12C and analyzing the data, insights into nuclear structure and the nature of interactions between particles can be gained.This study employs the Isospin Quantum Molecular Dynamics model (IQMD) to examine reaction cross-sections of collisions between various nuclei and 12C at specific energies.The calculated results show excellent agreement with experimental data. …”
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Prediction of thermal conductivity in CALF-20 with first-principles accuracy via machine learning interatomic potentials by Soham Mandal, Prabal K. Maiti

“…We use the Green-Kubo approach based on equilibrium molecular dynamics, with a heat-flux renormalization technique, to determine the thermal conductivity (κ) of CALF-20. …”
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6-Octadecenoic and Oleic Acid in Liquid Smoke Rice Husk Showed COVID-19 Inhibitor Properties by Ira Arundina, Neni Frimayanti, Meircurius Dwi Condro Surboyo, Theresia Indah Budhy, Benni Iskandar

“…Therefore, the molecular dynamics (MDs) simulation and pharmacophore analysis was performed to analyse the binding stability of 6-octadecenoic and oleic acid. …”
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Transport of Alzheimer's associated amyloid-β catalyzed by P-glycoprotein. by James W McCormick, Lauren McCormick, Gang Chen, Pia D Vogel, John G Wise

“…However, previous studies on the ability of P-gp to directly transport the Alzheimer's associated amyloid-β (Aβ) protein have produced contradictory results. Here we use molecular dynamics (MD) simulations, transport substrate accumulation studies in cell culture, and biochemical activity assays to show that P-gp actively transports Aβ. …”
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Heat Transport Hysteresis Generated Through Frequency Switching of a Time-Dependent Temperature Gradient by Renai Chen, Galen T. Craven

“…Analytical expressions are derived for the energy fluxes in/out of the system and the baths, with excellent agreement observed between the analytical expressions and the results from nonequilibrium molecular dynamics simulations. We find that the shape of the heat transport hysteresis curves can be significantly altered by shifting the frequency between fast and slow oscillation regimes. …”
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Wavelet Analysis of Shower Track Distribution in High-Energy Nucleus-Nucleus Collisions by Provash Mali, Soumya Sarkar, Amitabha Mukhopadhyay, Gurmukh Singh

“…For the first time, the wavelet results are compared with a model prediction based on the ultrarelativistic quantum molecular dynamics (UrQMD), where we adopt a charge reassignment algorithm to modify the UrQMD events to mimic the Bose-Einstein type of correlation among identical mesons—a feature known to be the most dominating factor responsible for local cluster formation. …”
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Comparing Standard Distribution and Its Tsallis Form of Transverse Momenta in High Energy Collisions by Rui-Fang Si, Hui-Ling Li, Fu-Hu Liu

“…The experimental (simulated) transverse momentum spectra of negatively charged pions produced at midrapidity in central nucleus-nucleus collisions at the Heavy-Ion Synchrotron (SIS), Relativistic Heavy-Ion Collider (RHIC), and Large Hadron Collider (LHC) energies obtained by different collaborations are selected by us to investigate, where a few simulated data are taken from the results of FOPI Collaboration which uses the IQMD transport code based on Quantum Molecular Dynamics. A two-component standard distribution and the Tsallis form of standard distribution are used to fit these data in the framework of a multisource thermal model. …”
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Clusters as a probe of the equation-of-state of strongly interacting matter by Gläßel Susanne, Voronyuk Vadim, Winn Michael, Kireyeu Viktar, Coci Gabriele, Aichelin Jörg, Blume Christoph, Bratkovskaya Elena

“…We investigate the influence of the equation-of-state (EoS) of strongly interacting matter created in heavy-ion collisions on the light cluster and hypernuclei production within the Parton-Hadron-Quantum-Molecular Dynamics (PHQMD) microscopic transport approach. …”
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Interference of a phytoconstituent from Nymphaea lotus-derived ligand N-acetyl glucosamine with signaling receptors in diabetes mellitus development: A targeted computational analy... by Sunday Amos Onikanni, Tran Nhat-Phong Dao, Adewale Oluwaseun Fadaka, Halliru Zailani, Oluwafemi Shittu Bakare, Omolola Esther Amos, Ashwil Klein, Valens Munyembaraga, Morenike Grace Ajayi, Adebola Iyabode Akinjokun, Babatunji Emmanuel Oyinloye, Leandro Miranda-Alves

“…Molecular docking studies, toxicity prediction, examination of drug depiction, and Molecular Dynamics Simulation (MDs) of the ligands with the identified receptor target were conducted using the Schrödinger platform. …”
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Extracting rates and activation free energies of martensitic transitions using nanomechanical force statistics: theory, models, and analysis by Arijit Maitra, M. P. Gururajan

“…Extensive sampling of the critical forces was performed using nonequilibrium molecular dynamics simulations of an atomic model of single-crystalline titanium nickel. …”
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Influence of oxygen on electronic correlation and transport in iron in the Earth’s outer core by Germán G. Blesio, Leonid V. Pourovskii, Markus Aichhorn, Monica Pozzo, Dario Alfè, Jernej Mravlje

“…We used a combination of molecular dynamics, density functional theory, and dynamical mean-field theory methods to examine the impact of oxygen impurities on the electronic correlations and transport in the Earth’s liquid outer core. …”
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Discovery of Novel Inhibitors for Nek6 Protein through Homology Model Assisted Structure Based Virtual Screening and Molecular Docking Approaches by P. Srinivasan, P. Chella Perumal, A. Sudha

“…The overall quality of computed model showed 87.4% amino acid residues under the favored region. A 3 ns molecular dynamics simulation confirmed that the structure was reliable and stable. …”
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Enhanced sampling of protein conformational changes via true reaction coordinates from energy relaxation by Huiyu Li, Ao Ma

“…These findings unlock access to a broader range of protein functional processes in molecular dynamics simulations.…”
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