Fast Algorithm for Quasi-2d Coulomb Systems DOI
Zecheng Gan,

Xuanzhao Gao,

Jiuyang Liang

et al.

Published: Jan. 1, 2024

Download This Paper Open PDF in Browser Add to My Library Share: Permalink Using these links will ensure access this page indefinitely Copy URL DOI

Language: Английский

Fast Algorithm for Quasi-2D Coulomb Systems DOI
Zecheng Gan,

Xuanzhao Gao,

Jiuyang Liang

et al.

Journal of Computational Physics, Journal Year: 2025, Volume and Issue: unknown, P. 113733 - 113733

Published: Jan. 1, 2025

Language: Английский

Citations

2

Energy stable scheme for random batch molecular dynamics DOI
Jiuyang Liang, Zhenli Xu, Yue Zhao

et al.

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 160(3)

Published: Jan. 16, 2024

The computational bottleneck of molecular dynamics is pairwise additive long-range interactions between particles. random batch Ewald (RBE) method provides a highly efficient and superscalable solver for interactions, but the stochastic nature this algorithm leads to unphysical self-heating effect during simulation. We propose an energy stable scheme (ESS) particle systems by employing Berendsen-type bath. removes notorious drift, which exists due force error even when symplectic integrator employed. Combining RBE with ESS, new perfect solution at microcanonical ensemble. Numerical results primitive electrolyte all-atom pure water demonstrate attractive performance algorithm, including its dramatically high accuracy, linear complexity, overcoming drift long-time simulations.

Language: Английский

Citations

3

Infinite Boundary Terms and Pairwise Interactions: A Unified Framework for Periodic Coulomb Systems DOI
Y. Zhao, Zhonghan Hu

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: June 3, 2025

The introduction of the infinite boundary terms and pairwise interactions [Hu, Z. J. Chem. Theory Comput. 2014, 10, 5254-5264] enables a physically intuitive approach for deriving electrostatic energy pressure both neutral non-neutral systems under periodic condition (PBC). For system consisting N point charges (with charge qj located at rj where j = 1, 2, ···, N) one distribution density ρ(r) within primary cell volume V, derived can be expressed as, Σi

Language: Английский

Citations

0

Rapid decomposition of methane hydrates induced by terahertz bidirectional pulse electric fields DOI

Yunhang Liang,

Xueqing Bi,

Yunlong Zhao

et al.

Energy, Journal Year: 2023, Volume and Issue: 286, P. 129633 - 129633

Published: Nov. 10, 2023

Language: Английский

Citations

7

Unveiling optimal wetting additives for extinguishing wood fires: Insights from molecular simulation and experimental investigations DOI
Junqing Meng,

Zihan Zhou,

Jie Wang

et al.

Surfaces and Interfaces, Journal Year: 2023, Volume and Issue: 44, P. 103805 - 103805

Published: Dec. 23, 2023

Language: Английский

Citations

6

Computational exploration of allosteric inhibitors targeting CDK4/CDK6 proteins: a promising approach for multi-target drug development DOI
Mahmood Khan, Kamaljot Singh, Sara Khan

et al.

Journal of Biomolecular Structure and Dynamics, Journal Year: 2024, Volume and Issue: unknown, P. 1 - 19

Published: Jan. 4, 2024

Cyclin-dependent kinases (CDKs) play a pivotal role in orchestrating the intricate regulation of cell cycle, fundamental process governing growth and division. In particular, CDK4 CDK6 are critical for transition from G1 phase to S phase, where Deoxyribonucleic acid (DNA) replication occurs, their dysregulation is linked various diseases, notably cancer. While ATP-binding site inhibitors CDKs well-documented, this study focuses on uncovering allosteric inhibitors, providing fresh perspective CDK inhibition. Computational techniques were employed investigation, utilizing Molecular Operating Environment (MOE) virtual screening drug-like compound library. Moreover, stability most promising binding was assessed through Dynamics (MD) simulations MMPBSA/MMGBSA analyses. The outcome reveals that three (C1, C2, C3) exhibited strongest affinity CDK4/CDK6, as corroborated by docking simulation computed energies ranged −6.1 −7.6 kcal/mol, underscoring potency these inhibitors. Notably, identifies key residues (PHE31, HIS95, HIS100, VAL101, ASP102, ASP104, THR107) roles mediating inhibitor within sites. Among findings, C1–CDK4 complex C2–CDK6 emerge particularly exhibiting high energies, favorable interaction patterns, sustained presence active site. This contributes significantly pursuit multi-target drugs against CDK4/CDK6 proteins, with potential implications development innovative therapies across disorders, including cancer other cycle-related conditions.

Language: Английский

Citations

0

Fast Algorithm for Quasi-2d Coulomb Systems DOI
Zecheng Gan,

Xuanzhao Gao,

Jiuyang Liang

et al.

Published: Jan. 1, 2024

Download This Paper Open PDF in Browser Add to My Library Share: Permalink Using these links will ensure access this page indefinitely Copy URL DOI

Language: Английский

Citations

0