Article
Physics, Fluids & Plasmas
Philipp Stroeker, Karsten Meier
Summary: The methodology developed by Lustig is applied to derive rigorous expressions for thermodynamic properties of fluids in the grand canonical ensemble, which are expressed by phase-space functions related to derivatives of the grand canonical potential. The derived expressions are validated by Monte Carlo simulations, providing more reliable results compared to previous literature and becoming equivalent to corresponding expressions in the canonical ensemble in the thermodynamic limit.
Article
Mechanics
Pipat Harata, Prathan Srivilai
Summary: We calculate the grand canonical partition function of a serial metallic island system using the imaginary-time path integral formalism. All electronic excitations in the lead and island electrodes are described using Grassmann numbers, and the Coulomb charging energy is represented in terms of phase fields. By using the large channel approximation, we determine the explicit phase dependence of the tunneling action. The partition function is represented as a path integral over phase fields, with a path probability given in an analytically known effective action functional. Additionally, we propose a method to calculate the average electron number and construct the quantum stability diagram of the serial island system using winding numbers.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2022)
Article
Chemistry, Physical
Xiangyuan Deng, Yun Liao, Meng Wang, Detao Xiao
Summary: Radon is a significant factor in the development of lung cancer. This study investigates the impact of pore size on the adsorption of radon by activated carbon (AC). Both simulations and experiments demonstrated that AC with a pore size of approximately 0.55 nm exhibited improved radon adsorption performance.
APPLIED SURFACE SCIENCE
(2024)
Article
Physics, Multidisciplinary
Tobias Dornheim
Summary: A practical analysis of the fermion sign problem in fermionic path integral Monte Carlo simulations in the grand-canonical ensemble showed that the sign problem in the GCE is more severe than in the canonical ensemble. Despite these challenges, fermionic PIMC simulations in the GCE are still feasible in many cases, providing access to important quantities for research fields such as warm dense matter, ultracold atoms, and electrons in quantum dots.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2021)
Article
Chemistry, Physical
Vitaly A. Gorbunov, Anastasiia I. Uliankina, Pavel Stishenko, Alexander Myshlyavtsev
Summary: The self-assembly of TPyB-Cu networks on MXene surface was investigated, revealing different local environments and thermal stabilities of metal-organic structures. The self-assembly offers opportunities for stabilizing and tuning catalyst properties.
APPLIED SURFACE SCIENCE
(2022)
Article
Chemistry, Physical
Jeongmin Kim, Luc Belloni, Benjamin Rotenberg
Summary: Molecular simulations that involve ion exchange in an open environment are important for studying various systems. A recent development in hybrid nonequilibrium molecular dynamics/Monte Carlo algorithms allows efficient computation of fluctuating number or charge density in dense fluids or ionic solutions. By optimizing electrostatic interactions and using bias-based methods, this approach significantly enhances the efficiency of salt-pair exchange in Lennard-Jones electrolytes.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Fluids & Plasmas
Cole Miles, Benjamin Cohen-Stead, Owen Bradley, Steven Johnston, Richard Scalettar, Kipton Barros
Summary: We present a method to simplify Monte Carlo simulations in the grand canonical ensemble by imposing a fictitious dynamics on the chemical potential. The method runs concurrently with the Monte Carlo sampling of the physical system and corrects the chemical potential based on time-averaged estimates of the mean and variance of the particle number. We performed various tests and found rapid convergence of the chemical potential in all cases, with the inexactness of the tuning algorithm contributing only a minor part of the total measurement error for realistic simulations.
Article
Chemistry, Physical
D. Caviedes, I. Cabria
Summary: In this study, the Grand Canonical Monte Carlo simulations were used to investigate the hydrogen storage capacities of different carbon nanopores shapes under various conditions. It was found that the storage capacities of pores increase with the curvature of the pores.
INTERNATIONAL JOURNAL OF HYDROGEN ENERGY
(2022)
Article
Nanoscience & Nanotechnology
Vrindaa Somjit, Bilge Yildiz
Summary: Identifying the structure of the Al2O3/Al interface is crucial for enhancing its performance in various applications. This study utilizes ab initio grand canonical Monte Carlo to explore the composition and configuration space of the interface, revealing its atomically sharp and layer-by-layer propagation nature. The insights obtained contribute to the design and engineering of Al2O3/Al-based corrosion coatings, controllable transistor technologies, and noise-free superconducting qubits.
ACS APPLIED MATERIALS & INTERFACES
(2022)
Article
Materials Science, Ceramics
Georgy Lazorenko, Anton Kasprzhitskii
Summary: A comparative study on water sorption by different components of the binder phase formed in geopolymerization was conducted using the GCMC simulation method. The results showed that structural changes in the host framework significantly affect water sorption properties. The simulation results provide valuable information on the behavior of water confined in geopolymeric binder phase, contributing to a better understanding of water adsorption mechanism.
CERAMICS INTERNATIONAL
(2022)
Article
Chemistry, Physical
Peng Bai, Matthew Neurock, J. Ilja Siepmann
Summary: This study utilizes first-principles grand-canonical simulations to predict water adsorption on H-ZSM-5 zeolites under specified experimental conditions, with the use of inexpensive force fields and a pool-based parallelization algorithm to improve simulation efficiency. The results show that H+ exchange significantly increases the hydrophilicity of zeolite MFI and a substantial amount of water is present even at very low relative humidities.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Biochemistry & Molecular Biology
Yunhui Ge, Oliver J. Melling, Weiming Dong, Jonathan W. Essex, David L. Mobley
Summary: Water plays a crucial role in protein-ligand interactions, but its slow rearrangement during binding can often hinder accurate free energy calculations. Previous studies have shown that grand canonical Monte Carlo (GCMC) simulations outperform normal molecular dynamics (MD) simulations in water sampling, but there is still room for improvement. In this work, we applied GCMC to evaluate its performance in rehydrating buried water sites in 21 protein-ligand systems. We found that while GCMC was successful in most systems, it failed in five systems due to protein/ligand motions obstructing water insertion. To overcome this, we extended our simulations and introduced a new technique called grand canonical nonequilibrium candidate Monte Carlo (GCNCMC), which showed promising results in rehydrating all target water sites in three out of the five problematic systems.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Article
Chemistry, Applied
Christopher Kessler, Johannes Eller, Joachim Gross, Niels Hansen
Summary: A classical density functional theory (cDFT) based on the PC-SAFT equation of state is proposed for the calculation of adsorption equilibria in covalent organic frameworks (COFs). The results show excellent agreement between PC-SAFT DFT and GCMC simulations for adsorption isotherms in COFs, indicating the predictive power of the method in selective accumulation of longer hydrocarbons in binary mixtures.
MICROPOROUS AND MESOPOROUS MATERIALS
(2021)
Article
Materials Science, Multidisciplinary
S. Sina Moeini-Ardakani, S. Mohadeseh Taheri-Mousavi, Ju Li
Summary: Interstitial alloying elements in metals play a crucial role in influencing their properties, but limitations in experimental and numerical tools hinder efforts to model these mechanisms effectively. Our efficient framework for hybrid simulations demonstrates significant improvements in computational cost and scalability compared to existing libraries.
MODELLING AND SIMULATION IN MATERIALS SCIENCE AND ENGINEERING
(2021)
Article
Chemistry, Physical
Mirjam Balbisi, Reka A. Horvath, Milan Szori, Pal Jedlovszky
Summary: The adsorption of acetamide on the surface of crystalline and low density amorphous ices was investigated under tropospheric conditions. The adsorption is primarily governed by the formation of new hydrogen bonds. The adsorption monolayer exhibits remarkable stability and forms a plateau in a broad range of chemical potential values.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Brianna D. Young, Wenbo Yu, Darex J. Vera Rodriguez, Kristen M. Varney, Alexander D. MacKerell, David J. Weber
Summary: S100B, a biomarker of malignant melanoma, interacts with the p53 protein and diminishes its tumor suppressor function, making it a promising therapeutic target for treating malignant melanoma. By combining NMR and computational approaches, insight was gained into designing specific inhibitors for S100A1 and S100B, improving drug design efforts to inhibit elevated S100B in melanoma. This fragment-based approach can be used to design specific inhibitors for other highly homologous drug targets.
Article
Chemistry, Physical
Anmol Kumar, Poonam Pandey, Payal Chatterjee, Alexander D. Jr Jr MacKerell
Summary: The Drude polarizable force field captures electronic polarization effects and is useful for simulating biomolecules and other molecules. Deep neural network models can accurately predict molecular dipole moments and polarizabilities.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Abhishek A. Kognole, Jumin Lee, Sang-Jun Park, Sunhwan Jo, Payal Chatterjee, Justin A. Lemkul, Jing Huang, Alexander D. MacKerell, Wonpil Im
Summary: The Drude Prepper tool has been developed in CHARMM-GUI to facilitate the use of polarizable FF based on the classic Drude oscillator model. It allows for easy construction of Drude FF-based PSF and generation of input for MD simulations using various simulation packages. The stability and effectiveness of the Drude Prepper protocol and inputs have been demonstrated through validation with a variety of heterogeneous systems.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2022)
Article
Chemistry, Physical
Adam T. Green, Amanda J. Pickard, Rongzhong Li, Alexander D. MacKerell, Ulrich Bierbach, Samuel S. Cho
Summary: This study uses circular dichroism spectroscopy to show the parallel topologies of two putative ribosomal G-quadruplex sequences, and validates and refines the modeled structures using molecular dynamics simulations. The results provide a structural foundation for understanding G-quadruplex functions and designing novel chemotherapeutics.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Review
Chemistry, Multidisciplinary
Himanshu Goel, Anthony Hazel, Wenbo Yu, Sunhwan Jo, Alexander D. MacKerell
Summary: SILCS utilizes molecular simulation to obtain functional group affinity patterns for drug discovery, allowing for identification of novel ligand binding pockets, prediction of protein-ligand binding affinities, and other applications in computer-aided drug design. It represents a comprehensive approach to improve drug development processes through accuracy and throughput enhancements.
NEW JOURNAL OF CHEMISTRY
(2022)
Article
Chemistry, Physical
Payal Chatterjee, Mert Y. Sengul, Anmol Kumar, Alexander D. MacKerell
Summary: The outcomes of computational chemistry and biology research are greatly influenced by the choice of forcefield used in molecular simulations. This study develops a deep learning-based framework for optimizing van der Waals interactions in molecular simulations. The resulting LJ parameters (interactions between atoms) are validated for their performance in reproducing condensed phase thermodynamic properties and demonstrate improved accuracy in reproducing solvent and crystal properties.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Medicinal
Asuka A. Orr, Suliman Sharif, Junmei Wang, Alexander D. MacKerell
Summary: Generalized force fields (FFs) are extensions of biomolecular FFs used for organic molecules. However, their application to arbitrary molecules requires caution to ensure their integrity.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2022)
Article
Chemistry, Physical
Abhishek A. Kognole, Anthony Hazel, Alexander D. MacKerell
Summary: RNA molecules can be potential drug targets in various diseases due to their dysregulated expression or misfolding. Noncoding RNAs, which account for a large part of the human genome, have complex structures and can be targeted by small molecules. The SILCS computational approach, termed SILCS-RNA, was extended to target RNA in this study and evaluated against seven RNA targets. The method provides detailed functional group affinity patterns and facilitates the identification of new potential binding sites and ligand design.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Wenbo Yu, David J. Weber, Alexander D. MacKerell
Summary: Covalent drug design plays a significant role in drug discovery by forming a covalent bond with targeted residues, leading to a more effective therapeutic approach. Computational methods can identify reactive residues, test potential reactivities, and predict noncovalent contributions to binding. SILCS, a functional group mapping approach, considers protein flexibility, functional group, and protein desolvation along with functional group-protein interactions. SILCS-Covalent, an integrated workflow, can qualitatively and quantitatively inform covalent drug discovery.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Yalun Yu, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor, Benoit Roux, Alexander D. MacKerell Jr, Jeffery B. Klauda
Summary: Accurate empirical force fields of lipid molecules are crucial for molecular dynamics simulations of various lipid systems and heterogeneous systems. The polarizable Drude force field has been optimized in this study to improve its accuracy in simulating pure bilayers and membranes. By using both experimental and quantum mechanical data, the optimized force field shows good agreement with a range of experimental observables. The polarizable Drude2023 force field is anticipated to advance our understanding of electronic polarization in lipid systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Mingtian Zhao, Abhishek A. Kognole, Sunhwan Jo, Aoxiang Tao, Anthony Hazel, Alexander D. MacKerell Jr
Summary: In this study, the sampling efficiency of the GCMC method was improved by applying known cavity-bias and configurational-bias algorithms on GPU architecture. The method was parallelized using CUDA and OpenCL, resulting in simultaneous sampling of a large number of configurations during insertion attempts. The partitioning scheme allowed for simultaneous insertion attempts for large systems, significantly improving efficiency. The algorithm was shown to be useful in the application of the site-identification by ligand competitive saturation (SILCS) co-solvent sampling approach for the protein CDK2.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Medicine, Research & Experimental
Asuka A. Orr, Aoxiang Tao, Olgun Guvench, Alexander D. MacKerell
Summary: Protein-based therapeutics often face challenges of protein aggregation and high solution viscosity due to high concentrations of active protein. The charge of a protein, affected by its environment, plays a significant role in these solution behaviors. This study presents a structure-based approach called SILCS-Biologics, which predicts the effective charge of proteins by considering the competition between ions and the presence of buffers.
MOLECULAR PHARMACEUTICS
(2023)
Article
Chemistry, Multidisciplinary
Mert Y. Sengul, Alexander D. MacKerell
Summary: Metal ions, particularly Mg2+, play a role in stabilizing RNA's tertiary structures. However, the atomic-level mechanisms underlying this process are not fully understood. In this study, computational techniques were combined to investigate the specific interactions between Mg2+ ions and RNA, particularly in the pseudoknot structure of the Twister ribozyme.
Article
Chemistry, Multidisciplinary
Himanshu Goel, Wenbo Yu, Alexander D. MacKerell
Summary: This article presents the application of structure- and ligand-based approaches in simulating and predicting hERG drug liability. By combining the SILCS method with physicochemical properties, predictive models for hERG blockade were developed, resulting in improved predictability and aiding in rational drug design to minimize hERG risk.
CHEMISTRY-SWITZERLAND
(2022)
Article
Chemistry, Multidisciplinary
Mert Y. Sengul, Alexander D. MacKerell
Summary: The presence of polarizability in the force field improves the stability of RNA hairpin structures and leads to variations in dipole moments and ion distribution. Molecular dynamics simulations play a crucial role in modeling biomolecular systems, and the treatment of electrostatic interactions in the force field strongly affects simulation accuracy. In this study, the impact of polarization on structural properties, dipole moment distributions, and cation interactions in RNA hairpin systems is investigated using polarizable and non-polarizable nucleic acid force fields.
JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY
(2022)