Article
Multidisciplinary Sciences
Jan Kessler, Francesco Calcavecchia, Thomas D. Kuehne
Summary: Inspired by the universal approximation theorem and the widespread adoption of artificial neural network techniques, feed-forward neural networks are proposed as a general purpose trial wave function for quantum Monte Carlo simulations of continuous many-body systems. The accuracy of the trial wave functions was demonstrated by studying an exactly solvable model system of two trapped interacting particles and the hydrogen dimer. The whole many-body wave function can be represented by a neural network for simple model systems, while the antisymmetry condition of non-trivial fermionic systems is incorporated by means of a Slater determinant.
ADVANCED THEORY AND SIMULATIONS
(2021)
Article
Polymer Science
Hana Ferkous, Karima Rouibah, Nour-El-Houda Hammoudi, Manawwer Alam, Chahrazed Djilani, Amel Delimi, Omar Laraba, Krishna Kumar Yadav, Hyun-Jo Ahn, Byong-Hun Jeon, Yacine Benguerba
Summary: This study investigated the adsorption mechanisms of methylene blue onto olive waste treated with KOH and onto a composite of KOH-treated waste and PEG-silica gel. The research found that electrostatic attraction and hydrogen bond formation are critical for the adsorption process.
Article
Chemistry, Physical
Robert F. Bull, Alfred C. K. Farris, David P. Landau
Summary: In this study, we investigated the thermodynamic and structural properties of synthetic multiblock copolymers using Wang-Landau sampling on a simple cubic lattice. We compared different sequences and observed differences in the collapse process, as well as studied structural transitions below the coil-to-globule transition temperature in the lattice. Additionally, we examined the relationship between block length, number of blocks, and overall polymer length with respect to these structural transitions, and observed how the formation and shape of a ground state core affected structural changes as temperature increased.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Wen Bin Kang, Lei Bao, Kai Zhang, Jia Guo, Ben Chao Zhu, Qian-Yuan Tang, Wei Tong Ren, Gen Zhu
Summary: This study investigates the impact of electrostatic repulsion and hydrophobic interactions on phase separation process using random peptides as model systems. It is found that stronger electrostatic repulsion leads to more extended single-chain structure and a higher likelihood of low-density homogeneous phase. On the other hand, stronger hydrophobic effect results in more compact single-chain structure, facilitating phase separation and increasing the critical temperature.
Article
Chemistry, Physical
Wen Bin Kang, Lei Bao, Kai Zhang, Jia Guo, Ben Chao Zhu, Qian-Yuan Tang, Wei Tong Ren, Gen Zhu
Summary: This study investigates the regulation mechanisms of electrostatic repulsion and hydrophobic interactions in the phase separation of proteins. The results reveal that stronger electrostatic repulsion leads to more extended single-chain structures and a higher probability of low-density homogeneous phase formation. On the other hand, stronger hydrophobic effect results in more compact single-chain structures, facilitating phase separation and increasing the critical temperature.
Article
Chemistry, Physical
Khaoula Laouameur, Abdenacer Flilissa, Alessandro Erto, Marco Balsamo, Barbara Ernst, Guilherme Dotto, Yacine Benguerba
Summary: The study investigates the removal of benzodiazepine (clorazepate, CLZ) from aqueous solution by adsorption onto maghnite clay, supported by theoretical simulations. The results show that adsorption is maximum at low pH, driven mainly by electrostatic interactions, and follows the pseudo-first-order kinetic model. The complementary theoretical study reveals that CLZ assumes a horizontal position on the maghnite surface upon adsorption, characterized by high energy adsorption.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Paola B. Torres, Pablo M. Blanco, Josep L. Garces, Claudio F. Narambuena
Summary: This study computes the electrostatic potential generated by a-lactoalbumin in the presence of added salt and investigates its fluctuations inside the protein. The calculations reveal that the fluctuations are mainly due to the asymmetric distribution of charge groups. The results also show good agreement with the Poisson equation and the Tanford-Kirkwood multipole expansion. Surprisingly, the linear Poisson-Boltzmann equation and Donnan potential provide accurate estimations of the average electrostatic potential on the protein surface. The partition coefficients predicted by Donnan theory also match well with the simulation results.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Inorganic & Nuclear
J. Attarki, M. Khnifira, W. Boumya, A. Mahsoune, E. M. Lemdek, M. Sadiq, M. Abdennouri, S. Kaya, N. Barka
Summary: In this study, the adsorption performance of MC on Zn3(PO4)2, Fe3(PO4)2, Co3(PO4)2, and Ca3(PO4)2 surfaces was investigated using MCD simulations and DFT. Quantum chemical descriptors and dynamic descriptors were calculated to understand the chemical properties of MC and its interaction mechanism with the adsorbent surfaces. The results showed that MC adsorbed parallelly on all surfaces and the adsorption was exothermic and spontaneous. The most stable adsorption configurations revealed chemisorption between the adsorbate and the surfaces, which was confirmed by RDF analysis.
INORGANIC CHEMISTRY COMMUNICATIONS
(2023)
Article
Chemistry, Physical
Stanislaw Lamperski, Lutful Bari Bhuiyan
Summary: Inverse Grand Canonical Monte Carlo simulations were used to calculate the entropy of a restricted primitive model electrolyte, considering the displacement of the cation charge centre. The results showed that the charge centre displacement and temperature increase led to an increase in entropy. The entropy as a function of concentration exhibited a turning point for different valency systems, indicating the presence of deformation caused by electrostatic and steric interactions. The type of ion also influenced the entropy change.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Biochemistry & Molecular Biology
Andrzej Patrykiejew
Summary: A simple lattice model was used to study the formation of multilayer films by fluids with orientation-dependent interactions on solid surfaces. The structure of multilayer films was found to depend on the strengths of surface potential felt by differently oriented particles and the interaction between the B halves of fluid particles. Finite temperature behavior was investigated through Monte Carlo simulation methods.
Article
Chemistry, Multidisciplinary
Ali Mohammadi, Ali Nakhaei Pour
Summary: This study investigates the impact of incorporating triethylenetetramine (TETA) into zeolitic imidazolate framework (ZIF-8) on CO2 adsorption capacity. The results show that TETA-impregnated ZIF-8 samples have slightly higher CO2 adsorption capacity than ZIF-8 at pressures lower than 2.5 bars, but as the pressure increases, ZIF-8 samples exhibit higher CO2 adsorption capacity compared to TETA-impregnated ZIF-8 samples.
JOURNAL OF CO2 UTILIZATION
(2023)
Article
Infectious Diseases
Yukihiro Hamada, Hidefumi Kasai, Moeko Suzuki-Ito, Yasufumi Matsumura, Yohei Doi, Kayoko Hayakawa
Summary: The optimal regimens for cefmetazole and flomoxef treatment in urinary tract infections caused by ESBL-producing Enterobacterales are not well established. This study found that the pharmacokinetic/pharmacodynamic targets for cefmetazole and flomoxef were 70% T > MIC, indicating bactericidal activity. Monte Carlo simulation was performed to calculate the probability of target attainment for different renal function groups. The results suggest different optimal dosages of cefmetazole and flomoxef for patients with different renal functions.
Article
Polymer Science
Claudio F. Narambuena, Pablo M. Blanco, Adrian Rodriguez, Diego E. Rodriguez, Sergio Madurga, Jose L. Garces, Francesc Mas
Summary: In this study, weak polyelectrolyte adsorption on a strong cationic surface was investigated using constant pH Monte Carlo simulations. The results showed a non-monotonic behavior of PE adsorbed amount with pH, and the apparent pKa(0) value of PE chains varied with pH and surface coverage. Additionally, the replacement of small anions with PE chains and small cations at higher pH values led to a significant charge reversion on the surface when pH was greater than pKa(0) + 1.
Article
Biochemistry & Molecular Biology
Joao N. C. Especial, Antonio Rey, Patricia F. N. Faisca
Summary: Monte Carlo simulations are a powerful technique used in various fields for sampling equilibrium ensembles and calculating thermodynamic and structural properties. The preservation of linear topology is crucial for obtaining correct equilibrium results, especially for complex structures.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Construction & Building Technology
Nicolas Krattiger, Barbara Lothenbach, Sergey Churakov
Summary: Alkali-silica reaction (ASR) is a significant factor in global concrete durability issues. Research shows that divalent ions can co-adsorb on C-S-H and ASR products under different pH and pore water chemistry conditions.
CEMENT AND CONCRETE RESEARCH
(2021)
Correction
Chemistry, Multidisciplinary
Yuri Gerelli, Amanda Eriksson Skog, Stephanie Jephthah, Rebecca J. L. Welbourn, Alexey Klechikov, Marie Skepo
Article
Biochemistry & Molecular Biology
Samuel Lenton, Stefan Hervo-Hansen, Anton M. Popov, Mark D. Tully, Mikael Lund, Marie Skepo
Summary: Re-entrant condensation occurs when a condensed protein regime forms between two critical ion concentrations. Attractive interactions between arginine and tripolyphosphate are found to determine the condensation and decondensation boundaries of cationic proteins. These findings provide insights into the organizational mechanism that can be used to tune protein interactions in solution.
Article
Chemistry, Physical
Eric Fagerberg, Samuel Lenton, Tommy Nylander, Tilo Seydel, Marie Skepo
Summary: This study investigates the dynamical properties of Histatin 5, an intrinsically disordered protein, under self-crowding conditions. Quasi-elastic neutron scattering and molecular dynamics simulations are used to analyze the diffusion behavior. The results show that diffusion decreases significantly under crowding, possibly due to aggregation at higher protein concentrations. The temperature effects largely follow Stokes-Einstein behavior. Simple geometric considerations fail to predict diffusion rates accurately, while simulations show some agreement with experiments. The scaling law previously used for globular proteins is found inadequate for Histatin 5, highlighting the distinct characteristics of intrinsically disordered proteins.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Multidisciplinary
Vidar Aspelin, Anna Lidskog, Carlos Solano Arribas, Stefan Hervo-Hansen, Bjorn Stenqvist, Richard Chudoba, Kenneth Warnmark, Mikael Lund
Summary: The consecutive binding of two potassium ions to BCETB in water was studied using experimental and simulation methods. A counterintuitive result was observed, with the enthalpy change associated with the binding of the second ion being more negative than that of the first ion. Further investigation revealed that the conformation of BCETB changes due to the coordination of potassium ions, which is related to the observed difference in enthalpy changes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Medicine, Research & Experimental
Sujata Mahapatra, Marco Polimeni, Lorenzo Gentiluomo, Dierk Roessner, Wolfgang Friess, Guenther H. J. Peters, Werner W. Streicher, Mikael Lund, Pernille Harris
Summary: The self-interactions of two monoclonal antibodies were studied using light scattering, small-angle X-ray scattering, and Monte Carlo simulations. By comparing simulation and experimental results, insights into the mAbs' self-interaction properties were obtained, with a focus on the role of ion binding and charged patches on the mAb surfaces. These models provide useful information about mAbs' self-interaction properties and assist in screening conditions for colloidal stability.
MOLECULAR PHARMACEUTICS
(2022)
Article
Chemistry, Physical
Atiyeh (Najla) Hosseini, Mikael Lund, Mohammad Reza Ejtehadi
Summary: This article introduces a correction Pair Forces method to improve the accuracy of NP-membrane translocation free energy calculations by calculating the forward and backward pulling forces for the Jarzynski free-energy estimator using steered molecular dynamics simulation.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Stefan Hervo-Hansen, Jan Heyda, Mikael Lund, Nobuyuki Matubayasi
Summary: The solvation of caffeine in different salts from the Hofmeister series was studied using molecular dynamics and energy-representation theory. The results showed that cations increased the solubility of caffeine by binding to the polar groups, while anions caused caffeine to aggregate by perturbing water. The excluded-volume effect was found to be the main mechanism for the perturbation of caffeine solvation by salt.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Maria Gunnarsson, Diana Bernin, Merima Hasani, Mikael Lund, Erik Bialik
Summary: The direct reaction between carbohydrates and CO2, resulting in the formation of cellulose carbonate, was confirmed using NMR spectroscopy. The study showed that CO2 reacts with not only the hydroxyl group on carbon 6 of cellulose. By comparing observed spectra with electronic structure calculations and using a simple computational method, good agreement between predicted and measured chemical shifts was found.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(2021)
Article
Chemistry, Physical
Coralie Pasquier, Soren Roi Midtgaard, Marco Polimeni, Christian Isak Jorgensen, Lise Arleth, Thomas H. Callisen, Mikael Lund
Summary: In this study, protein-protein interactions in protein solutions were investigated using small angle X-ray scattering and molecular simulations. The results showed that as protein concentration increases, the balance between spatial and orientational correlations changes, and patchy interactions may occur. By analyzing experimental data and simulations, it was found that patchy interactions between proteins lead to dimer formation, and these dimers exist in an open conformation, maximizing hydrophobic attractions for inter-protein alignment.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Correction
Chemistry, Multidisciplinary
Yuri Gerelli, Amanda Eriksson Skog, Stephanie Jephthah, Rebecca J. L. Welbourn, Alexey Klechikov, Marie Skepoe
Article
Chemistry, Medicinal
Eric Fagerberg, Marie Skepo
Summary: Coarse-graining is commonly used to reduce computational cost in simulations, but it is known to have lower transferability and accuracy for systems beyond its parametrization scope. In this study, we compared the performance of a bead-necklace model and a modified Martini 2 model, both coarse-grained models, using a set of intrinsically disordered proteins with different degrees of coarse-graining. The results showed that the naive expectation of the least coarse-grained model performing the best was not true, indicating that a more advanced model is not necessarily better in model choice.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Amanda E. Skog, Giacomo Corucci, Mark D. Tully, Giovanna Fragneto, Yuri Gerelli, Marie Skepo
Summary: Histatin 5 is a protein in saliva that acts as a defense against oral candidiasis. It forms a protein cushion under a model bilayer due to electrostatic interactions. Changing the number of histidines in the peptide sequence affects the penetration depth of the peptide into the bilayer.
Article
Chemistry, Physical
Simon Fridolf, Mona Koder Hamid, Leo Svenningsson, Marie Skepo, Emma Sparr, Daniel Topgaard
Summary: In this study, the impact of ganglioside GM3 on the bilayer structure and dynamics of C-H bond segments was investigated using solid-state NMR spectroscopy and molecular dynamics simulations. The findings revealed that GM3 affects the dynamical properties of POPC membranes, providing important insights into interactions with other biomolecules.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Atiyeh (Najla) Hosseini, Mikael Lund, Mohammad Reza Ejtehadi
Summary: Free-energy calculations are crucial for studying biomolecular interactions. The use of a Charge Switching model in this study significantly improves agreement between computational and experimental results, highlighting the importance of considering electronic polarization in free-energy calculations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Nanoscience & Nanotechnology
Sara Haddadi, Marie Skepo, Jan Forsman
Summary: In this study, polystyrene particles carrying short polyethylene glycol (PEG) chains were synthesized and the temperature-dependent aggregation and dispersion behavior was experimentally verified. Interestingly, repulsive polymer-mediated interactions were found at intermediate temperatures, while attractive interactions were observed at room temperature and high temperatures, leading to either flocculation or phase separation of particles. Fine-tuned theoretical models based on experimental results displayed semi-quantitative accuracy in predicting temperature-dependent stability of the system.
ACS NANOSCIENCE AU
(2021)