Article
Chemistry, Physical
Karol Palczynski, Thorren Kirschbaum, Annika Bande, Joachim Dzubiella
Summary: In this study, atomistically resolved molecular dynamics simulations were conducted using a reactive force field (ReaxFF) to characterize the interfacial water structure of hydrated diamondoids. The water structures were compared with different models, and it was found that the water molecules are most sensitive to the partial charges in the atomistically resolved diamondoids. Generic conclusions about the hydrophobic effect at nanoparticle interfaces were drawn, and the methods presented in this study can be applied to other hydrocarbons and interfacial systems.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Materials Science, Multidisciplinary
Lei Wei, Francisco J. Rodriguez-Fortuno
Summary: This study clarifies the discrepancy in torque calculation in prior literature and provides accurate expressions for the dipolar and quadrupolar torques based on first principles. The results are validated through numerical integration. The study also highlights the importance of distinguishing between the spin of the electromagnetic field gradient and the local electromagnetic field spin when calculating torque.
Article
Thermodynamics
Xiaowei Wang, Wenqing Zhang, Tianyi Su, Zhijun Zhang, Shiwei Zhang
Summary: The research reveals the significant impact of NEAC and TMAC variations on flow fields, thermal fields, pressure, and Knudsen force, with a nonlinear relationship observed between Knudsen force and NEAC as well as TMAC. Decreasing accommodation coefficients lead to an increase in the slope of the curve for Knudsen force, highlighting the sensitivity of these parameters to rarefied gas flows.
INTERNATIONAL JOURNAL OF HEAT AND MASS TRANSFER
(2021)
Article
Chemistry, Physical
Chunyu Li, Juan Carlos Verduzco, Brian H. Lee, Robert J. Appleton, Alejandro Strachan
Summary: The response of materials to shock loading is crucial for planetary science, aerospace engineering, and energetic materials. Deep learning is used to predict the resulting shock-induced temperature fields in composite materials, achieving higher accuracy and lower computation cost compared to current state of the art techniques.
NPJ COMPUTATIONAL MATERIALS
(2023)
Article
Physics, Multidisciplinary
Johannes Renner, Matthias Schmidt, Daniel de las Heras
Summary: The velocity field in a moving fluid is affected by its inherent viscous behavior, which helps to dampen any inhomogeneities. Both bulk and shear effects, related to the divergence and curl of the velocity field, play a role in this process. Memory also plays a significant role on molecular time scales beyond the Navier-Stokes description. Through molecular and overdamped Brownian dynamics many-body simulations, it has been demonstrated that similar viscous effects also act on the acceleration field, which can be quantitatively described using simple exponentially decaying memory kernels. The simultaneous use of velocity and acceleration fields allows for the description of fast dynamics on molecular scales.
PHYSICAL REVIEW LETTERS
(2022)
Article
Materials Science, Paper & Wood
Joel A. Sanchez-Badillo, Marco Gallo, Jose G. Rutiaga-Quinones, Pablo Lopez-Albarran
Summary: This study investigated the solvent behavior of a set of imidazolium-based ionic liquids around a crystallite model of cellulose I beta through molecular dynamics simulations. Results showed that the ionic liquids can disrupt the external chains of the cellulose crystallite and affect its properties such as density and vaporization enthalpy, contributing to cellulose preconditioning. Solvation free energy calculations for the cellulose chain revealed a specific trend among the different ionic liquids in their capacity for cellulose preconditioning.
Article
Computer Science, Artificial Intelligence
Oriel Kiss, Francesco Tacchino, Sofia Vallecorsa, Ivano Tavernelli
Summary: Accurate molecular force fields are crucial for efficient molecular dynamics techniques. Machine learning methods and quantum computers offer new solutions for predicting energy and forces. This study establishes a connection between classical and quantum solutions by designing a quantum neural network architecture, which successfully applies to molecules of increasing complexity.
MACHINE LEARNING-SCIENCE AND TECHNOLOGY
(2022)
Article
Polymer Science
Natalia Lukasheva, Dmitry Tolmachev, Hector Martinez-Seara, Mikko Karttunen
Summary: Electrostatic interactions play a crucial role in the behavior of polyelectrolyte molecules. This study investigated the behavior of anionic polyelectrolytes in water solutions using molecular dynamics simulations. Comparisons were made between different force fields, and the limitations and strengths of these force fields were determined based on experimental data. The results showed that the size and dynamics of the molecules depend on the models for the counterions, and the local structures and dynamics are sensitive to dihedral angle parameterization. Recommendations were made based on the findings.
Article
Computer Science, Artificial Intelligence
Cihat Duru, Hande Alemdar, Ozgur Ugras Baran
Summary: In this study, a new approach based on neural networks is proposed for estimating the pressure field around an airfoil, achieving a high accuracy of 88% for unseen airfoil shapes and significant speed-up compared to CFD simulations. The model allows for performance analysis of different airfoils and the effect of shock, showing promise in accurately capturing flow patterns.
NEURAL COMPUTING & APPLICATIONS
(2021)
Article
Chemistry, Physical
Atharva S. Kelkar, Bradley C. Dallin, Reid C. Van Lehn
Summary: Hydrophobic interactions play a crucial role in various biological and synthetic processes. This study demonstrates that the hydrophobicity of surfaces with chemically heterogeneous compositions can vary substantially depending on the spatial patterns and chemical identities of polar and nonpolar groups. The clustering of nonpolar groups is a common signature of highly hydrophobic patterns, and molecular dynamics analysis reveals its correlation with the perturbation of interfacial water structure.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Zun Wang, Hongfei Wu, Lixin Sun, Xinheng He, Zhirong Liu, Bin Shao, Tong Wang, Tie-Yan Liu
Summary: Machine learning force fields (MLFFs) have become a cost-effective alternative to ab initio molecular dynamics (MD) simulations. However, they suffer from generalization and robustness issues. To address this, we proposed global force metrics and fine-grained metrics to systematically measure MLFFs. We evaluated three state-of-the-art MLFFs on different molecules and analyzed the relationship between force metrics and simulation stability.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Materials Science, Multidisciplinary
Abdullah Bin Faheem, Kyung-Koo Lee
Summary: In the field of green energy production, molten salts have gained significant attention over the last few decades. Classical molecular dynamics (CMD) is a useful method for discovering and optimizing desirable molten salts, but the absence of CMD force fields that can accurately reproduce experimental physical properties poses a challenge. In this study, non-polarizable rigid ion models (RIMs) for widely used LiCl, KCl, and LiCl-KCl molten salts were developed using genetic algorithms (GAs). The results show that GAs are effective in optimizing force field parameters and the developed RIM force fields can reasonably reproduce experimental physical properties, providing microstructural characteristics similar to first-principles MD and improved overall performance at a lower computational cost. The developed atomwise RIM force fields with mixing rules for interactions between ions of different types reduce the total number of optimizable terms and enable transferability between different molten salt systems.
JOURNAL OF NUCLEAR MATERIALS
(2023)
Article
Chemistry, Physical
Angelina Folberth, Swaminath Bharadwaj, Nico F. A. van der Vegt
Summary: Our study investigates the impact of TMAO on the solvation of nonpolar solutes in water through MD simulations and free-energy calculations. We find that TMAO can exhibit a surfactant-like behavior, preferring to bind to large solutes and reducing the free-energy cost of solute-cavity formation. This behavior reinforces the solvent-mediated attraction between large solutes by means of an entropic force related to the accumulation of TMAO at interfaces.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Max L. Berkowitz
Summary: By utilizing an explicit charge transfer force field, simulations of aqueous salt solutions can accurately calculate the self-diffusion of water, providing quantitative agreement with experimental results. This suggests that the inclusion of charge transfer in force fields introduces new physics that were missing in previous simulations of aqueous electrolytes.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Marloes Arts, Victor Garcia Satorras, Chin-Wei Huang, Daniel Zuegner, Marco Federici, Cecilia Clementi, Frank Noe, Robert Pinsler, Rianne van den Berg
Summary: In this study, we employed score-based generative models and molecular dynamics to learn a force field for coarse-grained molecular dynamics. By training a diffusion generative model, we obtained an approximate force field that can be directly used to simulate coarse-grained molecular dynamics without requiring force inputs. Compared to previous work, our method significantly simplifies the training setup and demonstrates improved performance in protein simulations.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Biophysics
Martin Girard, Tristan Bereau
Summary: The plasma membrane acts as the interface between cells and the external environment, with lipid organization potentially influenced by different lipid chemical potentials. A new algorithm has been proposed to efficiently control the chemical nature of each lipid, allowing for the dynamic creation of asymmetric membranes. This algorithm is available as a plugin for the HOOMD-Blue molecular dynamics engine.
BIOPHYSICAL JOURNAL
(2021)
Article
Biophysics
Martin Girard, Tristan Bereau
Summary: The lipid-raft hypothesis suggests that cell membranes exhibit lateral organization, potentially due to a membrane critical point. A coherent framework using a lattice model demonstrates that lipid regulation can induce critical behavior in a complex membrane, leading to a wide temperature range of criticality. This framework provides strong support for the critical-membrane hypothesis without requiring specific sensing mechanisms.
BIOPHYSICAL JOURNAL
(2021)
Article
Chemistry, Physical
Marius Bause, Tristan Bereau
Summary: The article introduces a Maximum Caliber method for dynamical reweighting of complex systems, mapping trajectories to a Markovian description and reducing configurational space dimensionality to collective variables. This approach expands dynamical reweighting to larger systems and across a wide range of driving forces.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Biochemistry & Molecular Biology
Isabel S. Kleinwaechter, Stefanie Pannwitt, Alessia Centi, Nadja Hellmann, Eckhard Thines, Tristan Bereau, Dirk Schneider
Summary: The hydrophobic tails of aliphatic primary alcohols insert into the hydrophobic core of a lipid bilayer, disrupting interactions between lipid molecules and increasing membrane fluidity. Aromatic alcohols like 2-phenylethanol also impact membrane organization, and some derivatives have been shown to have bacteriostatic activities through their effects on biomembranes.
Correction
Chemistry, Physical
Arghya Dutta, Jilles Vreeken, Luca M. Ghiringhelli, Tristan Bereau
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Multidisciplinary Sciences
Matthias Scheffler, Martin Aeschlimann, Martin Albrecht, Tristan Bereau, Hans-Joachim Bungartz, Claudia Felser, Mark Greiner, Axel Gross, Christoph T. Koch, Kurt Kremer, Wolfgang E. Nagel, Markus Scheidgen, Christof Woell, Claudia Draxl
Summary: Achievements in condensed matter physics, chemistry, and materials science greatly influence the prosperity and lifestyle of our society, as new materials are crucial for various sectors. However, the value of the enormous amount of research data produced in these fields can only be realized through the establishment of a FAIR data infrastructure, allowing for comprehensive characterization and sharing of the data to advance science.
Article
Chemistry, Physical
Kiran H. Kanekal, Joseph F. Rudzinski, Tristan Bereau
Summary: Compared to top-down coarse-grained models, bottom-up approaches offer higher structural accuracy but may lack chemical transferability. This study presents a method that combines bottom-up, structure-preserving coarse-grained models with chemical transferability, using a set of CG bead types to construct new molecules.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Marc Stieffenhofer, Christoph Scherer, Falk May, Tristan Bereau, Denis Andrienko
Summary: In this study, the quality of different coarse-grained models is evaluated at the atomistic resolution using reverse-mapping strategies. Significant discrepancies between the all-atom and coarse-grained ensembles are revealed, and the reintroduced details allow for force computations and a clear ranking of the coarse-grained models.
FRONTIERS IN CHEMISTRY
(2022)
Article
Biophysics
Martin Girard, Tristan Bereau
Summary: The plasma membrane of eukaryotes exhibits lipid asymmetry, with different lipids primarily located in different leaflets. Using computational simulations, it has been found that saturation asymmetry arises as a result of phospholipid number asymmetry and sphingomyelin contents. This suggests that some asymmetries in lipid composition may naturally result from others and do not require external factors. The asymmetry of cholesterol, on the other hand, is fairly mild and influenced by all the other asymmetries.
BIOPHYSICAL JOURNAL
(2023)
Article
Chemistry, Physical
Bernadette Mohr, Diego van der Mast, Tristan Bereau
Summary: This study focuses on learning thermodynamic properties from molecular-liquid simulations using the Spectrum of London and Axilrod-Teller-Muto representation (SLATM).Through analysis of the preferential insertion of small solute molecules toward cardiolipin membranes and selectivity against a similar lipid, this methodology reveals interpretable relationships between two- and three-body interactions and selectivity, and provides a two-dimensional projection to display clearly separated basins.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Editorial Material
Multidisciplinary Sciences
Luca M. Ghiringhelli, Carsten Baldauf, Tristan Bereau, Sandor Brockhauser, Christian Carbogno, Javad Chamanara, Stefano Cozzini, Stefano Curtarolo, Claudia Draxl, Shyam Dwaraknath, Adam Fekete, James Kermode, Christoph T. Koch, Markus Kuehbach, Alvin Noe Ladines, Patrick Lambrix, Maja-Olivia Himmer, Sergey V. Levchenko, Micael Oliveira, Adam Michalchuk, Ronald E. Miller, Berk Onat, Pasquale Pavone, Giovanni Pizzi, Benjamin Regler, Gian-Marco Rignanese, Joerg Schaarschmidt, Markus Scheidgen, Astrid Schneidewind, Tatyana Sheveleva, Chuanxun Su, Denis Usvyat, Omar Valsson, Christof Woell, Matthias Scheffler
Summary: This paper presents the need for data sharing and repurposing in materials science and the importance of implementing the FAIR data principles. It focuses mainly on the FAIRification of computational materials science data and discusses the challenges related to experimental data and materials science ontologies.
Article
Materials Science, Biomaterials
Kuebra Kaygisiz, Arghya Dutta, Lena Rauch-Wirth, Christopher V. Synatschke, Jan Muench, Tristan Bereau, Tanja Weil
Summary: Amyloid-like nanofibers from self-assembling peptides have potential for therapeutic viral gene transfer. A machine learning approach was used to predict de novo sequences for viral infectivity enhancement, leading to the discovery of short but active peptides. This strategy is time- and cost-efficient for expanding the chemical space of self-assembling peptides.
BIOMATERIALS SCIENCE
(2023)
Article
Food Science & Technology
Arghya Dutta, Tristan Bereau, Thomas A. Vilgis
Summary: The amino acid sequence of a peptide is related to its taste, and specific patterns of amino acids have been identified for bitter and umami peptides. By extracting sequential amino acid patterns, the study helps locate taste-specific characteristics in peptides and proteins.
ACS FOOD SCIENCE & TECHNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Isabel Kleinwachter, Bernadette Mohr, Aljoscha Joppe, Nadja Hellmann, Tristan Bereau, Heinz D. Osiewacz, Dirk Schneider
Summary: Cardiolipin, a crucial lipid for stabilizing the inner mitochondrial membrane, can be targeted and controlled by a compound called CLiB, which affects the structure and function of mitochondrial membranes and proteins.
RSC CHEMICAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Bernadette Mohr, Kirill Shmilovich, Isabel S. Kleinwaechter, Dirk Schneider, Andrew L. Ferguson, Tristan Bereau
Summary: Subtle variations in lipid composition of mitochondrial membranes have a profound impact on mitochondrial function. This study combines deep learning-enabled active learning, molecular dynamics simulations, and free energy calculations to discover small organic compounds that can selectively permeate cardiolipin-containing membranes. The findings highlight the potential of coarse-grained representations and multiscale modeling for materials discovery and design.
