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
Chemistry, Physical
Hiromune Wada, Yuko Okamoto
Summary: In this study, we proposed a method to extend the fast weight determination scheme to two-dimensional space, considering both temperature and pressure. By self-updating weight parameters, a uniform random walk in the entire temperature-pressure space was achieved.
Article
Chemistry, Physical
Keita Kobayashi, Yuki Nagai, Mitsuhiro Itakura, Motoyuki Shiga
Summary: SLHMC is a self-learning hybrid Monte Carlo simulation method that allows for exact ensemble generation on potential energy surfaces based on density functional theory, with smart trial moves by machine learning potentials to accelerate statistical sampling; the method is extended from canonical sampling to isothermal-isobaric ensembles for studying the vibrational structure of soft materials and liquids, showing good agreement with high-energy X-ray data.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Taichi Inagaki, Shinji Saito
Summary: In this paper, a new hybrid method called potential scaling HMC (PS-HMC) is introduced to study complex chemical processes. By modulating the trajectory and gradually flattening the potential energy surface, the PS-HMC method is capable of constructing the canonical ensemble with a multimodal distribution. Applications to different molecular processes demonstrate the feasibility and features of this new method.
JOURNAL OF CHEMICAL PHYSICS
(2022)
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
Chemistry, Multidisciplinary
Roderick Corstiaan Abraham Versloot, Patricia Arias-Orozco, Matthijs Jonathan Tadema, Florian Leonardus Rudolfus Lucas, Xinghong Zhao, Siewert J. J. Marrink, Oscar Paul Kuipers, Giovanni Maglia
Summary: Mass spectrometry cannot distinguish between molecules with the same mass-to-charge ratio, but nanopore technology can differentiate diastereomeric and enantiomeric differences in peptides that cannot be observed by conventional MS analysis. The resolution in nanopore analysis is likely due to multiple chiral interactions during peptide transport across the nanopore, similar to chiral chromatography. Nanopore technology also offers possibilities for the rapid and cost-effective analysis of peptides, including those that cannot be easily differentiated by mass spectrometry.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Polymer Science
Emmanuel N. Skountzos, Katerina S. Karadima, Vlasis G. Mavrantzas
Summary: The study investigates the impact of adsorbed domains and nanoparticle bridging chains on the properties of attractive polymer nanocomposite melts through MD simulations. The presence of adsorbed polymer significantly affects the dynamic and conformational properties of the nanocomposite, especially under conditions favoring higher surface-to-volume ratios. Moreover, the bridging chains drive the formation of a nanoparticle network which becomes denser and stronger with increasing concentration of the polymer matrix in nanoparticles.
Article
Physics, Fluids & Plasmas
Andrey Pereverzev
Summary: This paper derives expressions for classical isothermal and adiabatic elastic constants with explicit boundary contributions and compares the results obtained using two different forms of the Born term. The study shows that the new form of the Born term involving only first derivatives of atomic-group or total potential energies converges to the same value as the original Born term but at a slower rate.
Article
Chemistry, Physical
Austin R. Dulaney, Stewart A. Mallory, John F. Brady
Summary: This study demonstrates that the mechanically defined isothermal compressibility behaves as a thermodynamic response function for suspensions of active Brownian particles. The equivalence between mechanical compressibility and static structure factor, as indicated by the active form of the thermodynamic compressibility equation, holds true even when activity is large. The importance of phase interface in defining an active chemical potential is highlighted, with previous definitions accurate above the critical point but breaking down in the coexistence region.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Materials Science, Multidisciplinary
Alois Castellano, Francois Bottin, Johann Bouchet, Antoine Levitt, Gabriel Stoltz
Summary: The paragraph introduces a method called machine learning assisted canonical sampling, which accelerates the sampling of the Born-Oppenheimer potential surface in the canonical ensemble, with a lower computational cost to replicate the results of ab initio molecular dynamics (AIMD).
Article
Chemistry, Physical
Yawen Miao, Kai Chen, Xu Zhang, Zhijun Xu, Xiaoning Yang
Summary: Studying the interaction of ionized two-dimensional graphene oxide (GO) nanosheets at the air-water interface revealed that GO nanosheets with the same negative charge can attract each other at the interface, in contrast with repulsive interaction in the bulk phase. This attractive interaction is attributed to an enhanced solvation force arising from shared bridge water structure at the interface between negatively charged GO sheets.
JOURNAL OF PHYSICAL CHEMISTRY C
(2021)
Article
Chemistry, Medicinal
Nitin A. Patil, Wendong Ma, Xukai Jiang, Xiaoji He, Heidi H. Yu, Hasini Wickremasinghe, Jiping Wang, Philip E. Thompson, Tony Velkov, Kade D. Roberts, Jian Li
Summary: Polymyxins, including polymyxin B and colistin, are used as a last resort to treat life-threatening multidrug-resistant Gram-negative bacterial infections. However, their clinical use is limited by toxicity and increasing resistance. This study explores the role of the conserved position 10 threonine residue in polymyxin's structure and reveals the requirements for antibacterial activity. These findings provide vital information for developing safer and more effective next-generation polymyxin antibiotics.
JOURNAL OF MEDICINAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
Hamed Emamy, Francis W. Starr, Sanat K. Kumar
Summary: Strong attractions between polymer-nanoparticles can lead to the spontaneous formation of a polymer layer with distinct dynamic characteristics at the nanoparticle interface. When investigating how nanoparticle mobility affects the signature of the bound layer, it was found that for small, relatively mobile nanoparticles, the bound layer is linked to the motion of the nanoparticle, causing the relaxation signature of the bound layer to essentially disappear in the intermediate scattering function.
Article
Chemistry, Physical
Jerome Rey, Sarah Blanck, Paul Clabaut, Sophie Loehle, Stephan N. Steinmann, Carine Michel
Summary: The paper introduces a new method based on Gaussian Lennard-Jones potential for simulating interactions between organic molecules and oxide surfaces. Molecular dynamics simulations were used to study the interactions of oxygenated and amine molecules with hematite and gamma-alumina surfaces, showing that the GLJ potential has better performance than traditional methods.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Analytical
Helisa H. Wippel, Juan D. Chavez, Andrew D. Keller, James E. Bruce
Summary: The XL-MS technique provides insight into protein conformations and interactions within their cellular environment, while the iqPIR strategy allows for comparative interactome studies using isotope encoded chemical cross-linkers. Multiplexed iqPIR enables quantitative interactome analysis of up to six biological samples in a single LC-MS acquisition, revealing specific protein conformational and interaction changes in response to different inhibitors.
ANALYTICAL CHEMISTRY
(2022)
Article
Engineering, Chemical
Cunkui Huang, Craig Hawrelechko, James Donald, Haibo Huang, Xiaohui Deng
Article
Mechanics
Oladapo Ayeni, Shashank S. Tiwari, Chunliang Wu, Jyeshtharaj B. Joshi, Krishnaswamy Nandakumar
Article
Polymer Science
Jianmei Wang, Xueying Wang, Yan Li, Hongyu Si, Chengmin Chen, Jianchun Wang, Zongjun Long, Krishnaswamy Nandakumar
Article
Chemistry, Multidisciplinary
Pingan Zhu, Chengmin Chen, Krishnaswamy Nandakumar, Liqiu Wang
Summary: Adding a dimple on super-repellent surfaces can break the symmetries in the law of reflection, allowing for fine tuning of droplet translational velocity in both direction and magnitude. This enables versatile droplet manipulation including trapping, shedding, antigravity transport, targeted positioning, and on-demand coalescence of droplets.
Article
Engineering, Chemical
Zhizhong Ding, Shashank S. Tiwari, Mayank Tyagi, Krishnaswamy Nandakumar
Summary: The study demonstrates that while the simulated bubble patterns show regularity, the actual arrangement of bubbles is unstable. Additionally, the prediction of bubble patterns is affected by the mathematical limitations of frictional closure models.
CANADIAN JOURNAL OF CHEMICAL ENGINEERING
(2022)
Article
Engineering, Chemical
Yuxiu Li, Shashank S. Tiwari, Geoffrey M. Evans, Krishnaswamy Nandakumar, Jyeshtharaj B. Joshi
Summary: Direct Numerical Simulations (DNS) using a non-Lagrangian multiplier based fictitious domain (FD) method were conducted to study the behavior of freely falling/rising rigid particles in a quiescent fluid. The simulations validated well against experimental results and identified several distinct flow regimes, including helical and zig-zagging trajectories for different solid-to-fluid density ratios. Fast Fourier Transform (FFT) analysis revealed a bimodal frequency pattern similar to flow past an isolated stationary bluff body.
INTERNATIONAL JOURNAL OF CHEMICAL REACTOR ENGINEERING
(2021)
Article
Engineering, Chemical
Chengmin Chen, Zhizhong Ding, Shashank S. Tiwari, Jianmei Wang, Jianchun Wang, Guangxia Liu, Yan Li, Meng Guo, Krishnaswamy Nandakumar
Summary: The impingement process of alginate droplet on an immiscible liquid was investigated using experimental and numerical approaches, revealing that the intensity of interaction between the two liquids leads to different droplet shapes. The droplet yield stress, Ohnesorge number, and Weber number were identified as key parameters determining the droplet shape.
CANADIAN JOURNAL OF CHEMICAL ENGINEERING
(2022)
Article
Engineering, Chemical
Zhizhong Ding, Shashank S. Tiwari, Chenguang Zhang, Mayank Tyagi, Bo Kong, Krishnaswamy Nandakumar, Jyeshtharaj B. Joshi
Summary: This study investigates the dynamic response of a neutrally buoyant elliptical cylinder in shear flow, revealing two distinct responses and discussing the transition between them through the prediction of a critical Reynolds number. The findings validate the effectiveness of the SDFIBM method for particles subjected to shear flows.
CANADIAN JOURNAL OF CHEMICAL ENGINEERING
(2022)
Article
Energy & Fuels
C. Zhang, Andrew N. Okafor, Hiba Malik, K. D. P. Nigam, K. Nandakumar
Summary: This study evaluates the Toroidal Helical Pipe (THP) as a means of process intensification compared to an equivalent length of straight pipe. The THP provides continuous curvature changes that result in complex secondary flows, effectively reducing concentration polarization.
CHEMICAL ENGINEERING AND PROCESSING-PROCESS INTENSIFICATION
(2022)
Article
Engineering, Chemical
Timothy A. Sipkens, Una Trivanovic, Arash Naseri, Olanrewaju W. Bello, Alberto Baldelli, Mohsen Kazemimanesh, Allan K. Bertram, Larry Kostiuk, Joel C. Corbin, Jason S. Olfert, Steven N. Rogak
Summary: The study examined the mixing state of aerosol produced by a laboratory flare with and without entrained droplets of sodium chloride solutions, finding that the majority of soot particles were internally mixed with salt, but there were also a large number of isolated salt particles.
JOURNAL OF AEROSOL SCIENCE
(2021)
Article
Chemistry, Analytical
Pei Zhao, Jianchun Wang, Chengmin Chen, Jianmei Wang, Guangxia Liu, Krishnaswamy Nandakumar, Yan Li, Liqiu Wang
Summary: This article introduces the applications of microfluidic technology in drug development, focusing on the recent developments and trends in microfluidic fabrication of drug carriers and microfluidic chips for drug toxicity screening. The challenges and future directions of microfluidic applications in drug development are also discussed.
Article
Engineering, Chemical
Anil K. Mehrotra, Joao B. P. Soares, Krishnaswamy Nandakumar, Pierre J. Carreau, Norman Epstein, Gregory S. Patience
Summary: The history and achievements of The Canadian Journal of Chemical Engineering highlight the multifaceted development of chemical engineering and its crucial role in advancing chemical sciences and engineering.
CANADIAN JOURNAL OF CHEMICAL ENGINEERING
(2022)
Article
Engineering, Chemical
Krishnaswamy Nandakumar, Mayank Tyagi, Ye Xu, Kalliat T. Valsaraj, Jyeshtharaj B. Joshi
Summary: Through introspection and assessment, the chemical engineering field has developed a mature undergraduate curriculum that equips engineers with skills in transport, reaction engineering, and thermodynamics. However, there is a need to adapt the curriculum to meet the needs of established industries while nurturing innovators for emerging industries, without harming the field unintentionally.
CANADIAN JOURNAL OF CHEMICAL ENGINEERING
(2022)
Article
Engineering, Multidisciplinary
Ahmed M. Alatyar, Abdallah S. Berrouk, Mohamed S. Alshehhi, Muhammed Saeed, Haitem Hassan-Beck, Krishnaswamy Nandakumar
Summary: The current study aims to enhance the hydraulic performance of Rotating Packed Beds (RPB) by modifying the geometrical construction of the inner cavity, outlet pipe, and packing. Four novel geometries of the RPB were proposed and analyzed using a validated CFD model, and it was found that optimizing the flow pattern at the exit of the packing by modifying the inner cavity's shape can reduce the total pressure drops by up to 22%. The addition of a nozzle at the entry of the outlet pipe further decreases the pressure drop by 13%.
ALEXANDRIA ENGINEERING JOURNAL
(2023)
Article
Multidisciplinary Sciences
James Tatum, Ambuj Punia, Larry Kostiuk, Marc Secanell, Jason Olfert
Summary: Methane pyrolysis is a process that produces hydrogen gas and carbon black without generating carbon dioxide. The study investigated the effects of temperature and reaction time on hydrogen molar concentration. The results showed that the hydrogen concentration increased with higher temperature and longer reaction time.
Article
Chemistry, Physical
B. P. Akhouri, R. Perween, J. R. Solana
Summary: Monte Carlo simulations are used to obtain the equation of state and internal energy of fluids with Mie n-m potentials, and its performance is tested against a third order perturbation theory. The theory is then applied to tune the potentials for real fluids and achieve accurate fit with experimental data.
MOLECULAR SIMULATION
(2024)
Article
Chemistry, Physical
Malaisamy Veerapandian, Nagarajan Hemavathy, Alagesan Karthika, Jayaraman Manikandan, Umashankar Vetrivel, Jeyaraman Jeyakanthan
Summary: This study investigates the conformational stability and flexibility of SpeB enzyme and its interactions with substrate. The research finds that neutral pH 7 and alkaline pH 11 are the optimal conditions for stable binding between SpeB and substrate.
MOLECULAR SIMULATION
(2024)
Article
Chemistry, Physical
Maipelo Nyepetsi, Olayinka A. Oyetunji, Foster Mbaiwa
Summary: Biodiesel, a potential alternative to fossil-based fuels, has limitations such as high viscosity, pour point, and cloud point. This study used ReaxFF molecular dynamics to investigate the decarboxylation of methyl palmitate using different catalysts. The presence of alpha-NiMoO4 and beta-NiMoO4 accelerated the reactions and resulted in higher quantities of stable products. Ni3Mo catalyst showed an initial rapid formation of products followed by a decrease. All reactions followed first-order kinetics, and the catalysts reduced the activation energies.
MOLECULAR SIMULATION
(2024)