Article
Construction & Building Technology
Yong Tao, Siavash Zare, Fazhou Wang, Mohammad Javad Abdolhosseini Qomi
Summary: Low-temperature cement manufacturing attracts attention for its low environmental impact, but slow hydration kinetics affects early-age strength development. This study uses rare event sampling techniques to uncover the mechanism of calcium ion dissolution from a kink site, and calculates the rate and equilibrium constants for each reaction step.
CEMENT AND CONCRETE RESEARCH
(2022)
Article
Chemistry, Physical
Maryam Reisjalali, Rex Manurung, Paola Carbone, Alessandro Troisi
Summary: Decades of work have shown the challenges of generating equilibrated models for semiconducting polymers, especially due to the anisotropic nature of their interactions. A rapid hybrid model generation procedure is introduced in this study, which proves to be accurate for two out of three cases considered. The hybrid representation can be used to directly evaluate the electronic properties of structures sampled by simulations.
MOLECULAR SYSTEMS DESIGN & ENGINEERING
(2022)
Article
Chemistry, Multidisciplinary
Julian A. C. Stein, Alan Ianeselli, Dieter Braun
Summary: MST is a versatile technique for measuring binding affinities, based on directional movement of molecules in a temperature gradient. We extended MST to measure binding kinetics by increasing thermal dissipation, allowing for simultaneous determination of kinetics and binding affinity. By measuring DNA hybridization rates, we observed linear dependence of on-rates on salt concentration and weak dependence on strand length and temperature.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Multidisciplinary
Timothy Connor, Oskar Cheong, Thomas Bornhake, Alison C. Shad, Rebekka Tesch, Mengli Sun, Zhengda He, Andrey Bukayemsky, Victor L. Vinograd, Sarah C. Finkeldei, Piotr M. Kowalski
Summary: Pyrochlore compounds have wide applicability in science and technology, and this study focuses on simulation-based efforts to accurately compute properties of these compounds. The research investigates dopant incorporation, defect formation, anion migration, and order-disorder transitions, as well as the incorporation of actinide elements into pyrochlores. The synergy of computed and experimental data provides a superior characterization of pyrochlores not easily achieved by either method alone.
FRONTIERS IN CHEMISTRY
(2021)
Article
Biochemistry & Molecular Biology
Loan Huynh, Alan Chen
Summary: The concentrations of specific macromolecular species can be quantified using diagnostic tools that rely on molecular recognition by nucleic acid aptamers. This article introduces a method for highly sensitive detection of serum thrombin levels using osmium tetroxide 2,2'-bipyridine protein adducts and electrochemical detection. The DNA aptamer is modified to enhance its binding affinity for thrombin.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Energy & Fuels
Piotr M. Kowalski, Zhengda He, Oskar Cheong
Summary: This paper discusses the thermodynamic properties of LixFePO4 and stabilizing zirconia compounds, showing different chemical characteristics under various conditions and having the potential for widespread application in energy storage.
FRONTIERS IN ENERGY RESEARCH
(2021)
Article
Chemistry, Physical
Matic Poberznik, Gabriela Herrero-Saboya, Darko Makovec, Darja Lisjak, Layla Martin-Samos
Summary: Barium hexaferrite (BHF) is a ferrimagnet that grows as platelets at the nanoscale, showing uniaxial magnetic anisotropy. The surface morphology of BHF nanoplatelets varies depending on the preparation conditions. Using ab initio thermodynamics, we found that the most stable surface terminations of BHF are the hydroxylated oxygen-terminated surfaces (12k-O) under Ba-poor and low pH conditions, and the hydroxylated 2b surface under high pH and Ba-rich conditions.
APPLIED SURFACE SCIENCE
(2023)
Article
Materials Science, Ceramics
Paul C. M. Fossati, Thomas A. Mellan, Navaratnarajah Kuganathan, William E. Lee
Summary: A study was conducted on the vibration modes and thermodynamical properties of amorphous sodium silicate using atomic-scale models and considering different Na2O concentrations. The potentials used showed the ability to describe various oxides, suggesting potential for studying more complex glasses in the future.
JOURNAL OF THE AMERICAN CERAMIC SOCIETY
(2021)
Article
Polymer Science
Shreya Shetty, Enrique D. Gomez, Scott T. Milner
Summary: The study used molecular dynamics simulations and morphing method to calculate the interaction parameter chi for real polymer blends, with different transformation schemes needed for different polymers. Predictions for the first three blends agree reasonably with experiments but are sensitive to force field parameters.
Article
Chemistry, Multidisciplinary
Matteo Erbi, Hakim Amara, Riccardo Gatti
Summary: Understanding the mechanical properties of metallic nanoparticles is crucial for their applications. Atomic-scale and continuous calculations are used to analyze gold nanoparticles and reveal that the elastic properties are influenced by their shape rather than size. A descriptor is introduced to distinguish different nanoparticle shapes. The same dependence on shape is observed for copper and platinum nanoparticles, highlighting the universality of the findings.
Article
Chemistry, Physical
Leonard P. Heinz, Helmut Grubmuller
Summary: The study presents a new method called Per|Mut, which utilizes permutation reduction and mutual information expansion to address the sampling problem of hydration entropy. The method was tested on various systems, including an argon system, solvated n-alkanes, and solvated octanol.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Review
Chemistry, Multidisciplinary
Johannes T. Margraf
Summary: Machine learning algorithms are powerful tools in science, but large well-curated databases are sparse in chemistry. This contribution reviews science-driven machine learning approaches that focus on atomistic modelling of materials and molecules. Science-driven machine learning involves starting with a scientific question and determining appropriate training data and model design choices. It emphasizes automated and purpose-driven data collection, the use of chemical and physical priors for efficient data usage, and the importance of appropriate model evaluation and error estimation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Pramod Bhingardeve, Prashant Jain, Krishna N. Ganesh
Summary: Peptide nucleic acids (PNAs) are DNA analogues with superior stability and specificity in binding to DNA or RNA. The newly developed bimodal PNAs (bm-PNA) can form double duplexes and have potential for generating novel higher-order assemblies. The C gamma-bimodal PNAs show increased stability in complex formation with DNA and exhibit low toxicity in cell studies.
Article
Chemistry, Multidisciplinary
J. Alfredo Freites, Mohab N. N. Louis, Douglas J. J. Tobias
Summary: Using atomistic multiscale molecular simulations, we investigated the solution-state conformational dynamics and interprotein interactions of ?D-crystallin and its P23T-R36S mutant. We found that the mutant retains the protein fold but exhibits changes in surface exposure of residues, leading to enhanced protein-protein interactions and specific contacts observed in the protein crystal lattice.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Delin Sun, Stewart He, W. F. Drew Bennett, Camille L. Bilodeau, Olaf S. Andersen, Felice C. Lightstone, Helgi I. Ingolfsson
Summary: Research on gramicidin A (gA) subunit dimerization in lipid bilayers revealed a dimer structure with two subunits connected by six hydrogen bonds, as well as two additional dimer structures stabilized by four or two hydrogen bonds. The temporal evolution study found that the dimer can form directly with six hydrogen bonds, or through paths involving two or four hydrogen bonds.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Biographical-Item
Multidisciplinary Sciences
Pablo G. Debenedetti, Peter H. Poole, Srikanth Sastry, Francesco Sciortino
Article
Materials Science, Multidisciplinary
Charles Emmett Maher, Frank H. Stillinger, Salvatore Torquato
Summary: This study investigates the dense packings of a class of nonspherical particles and examines their structure and properties. The results show that these superball packings exhibit hyperuniformity and nonanalytic behavior, with some common patterns observed among different shapes of superballs. These findings are important for the design of granular or colloidal materials with specific densities and transport properties.
PHYSICAL REVIEW MATERIALS
(2022)
Article
Chemistry, Physical
Thomas E. Gartner, Kelly M. Hunte, Eleftherios Lambros, Alessandro Caruso, Marc Riera, Gregory R. Medders, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti, Francesco Paesani
Summary: In this study, molecular dynamics simulations with the many-body MB-pol model were used to investigate the thermodynamic response and local structure of liquid water at different temperatures. The results suggest that the MB-pol model has predictive capability for the physical properties of liquid water across a wide range of thermodynamic states, including the difficult-to-probe "water's no man's land."
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Jack Weis, Francesco Sciortino, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti
Summary: Recent experiments and numerical simulations have provided support to the hypothesis that a second critical point exists in deeply supercooled water. In particular, a study has found that a liquid-liquid critical point can be located using a model parameterized solely based on ab initio calculations. This finding is important for understanding the phase behavior of supercooled water.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Yiming Wang, Frank H. Stillinger, Pablo G. Debenedetti
Summary: In this study, molecular dynamics simulations were performed to investigate the fluid-fluid phase transitions of a flexible three-dimensional four-site chiral molecular model. By introducing bias favoring local homochiral vs heterochiral interactions, the system exhibited a phase transition from a single achiral phase to a single chiral phase, with infrequent interconversion between the two chiral states. The results provide basic thermodynamic and kinetic insights for understanding many-body chiral symmetry breaking phenomena.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Pablo M. Piaggi, Jack Weis, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti, Roberto Car
Summary: Molecular simulations based on machine-learning models and density-functional theory have provided insights into the mechanism of homogeneous ice nucleation. The results are in good agreement with experimental measurements, and the impact of factors such as thermodynamic driving force, interfacial free energy, and stacking disorder on nucleation rates has been studied.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Nikolai D. Petsev, Arash Nikoubashman, Folarin Latinwo, Frank H. Stillinger, Pablo G. Debenedetti
Summary: Chiral crystals and their constituent molecules are important in theories about the origin of biological homochirality and in drug discovery, design, and stability. The prediction and identification of stable chiral crystal structures is complicated by many body interactions and molecular complexity. This study uses genetic algorithms to predict crystal lattices formed by a chiral tetramer molecular model and explores the stability and structures of conglomerate and racemic crystals.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Article
Chemistry, Physical
Haina Wang, Frank H. Stillinger, Salvatore Torquato
Summary: The Zhang-Torquato conjecture states that any realizable set of pair statistics, whether from a nonequilibrium or equilibrium system, can be achieved by equilibrium systems involving up to two-body interactions. The study shows that the unit-step function g(2) can be easily realized within a certain range of densities. For higher dimensions, the maximum terminal packing fraction can be achieved, and the large-r behaviors of the effective potentials are given by approximate expressions based on known conditions. These findings are important for the design of novel nanoparticle systems with density-dependent effective potentials, including exotic hyperuniform states of matter.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Physics, Multidisciplinary
Thomas E. Gartner III, Pablo M. Piaggi, Roberto Car, Athanassios Z. Panagiotopoulos, Pablo G. Debenedetti
Summary: The study provides preliminary evidence of liquid-liquid phase transition in water using molecular simulation techniques and a neural network model based on density functional theory calculations.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Thomas J. Longo, Nikolay A. Shumovskyi, Betul Uralcanc, Sergey. V. V. Buldyrev, Mikhail A. Anisimov, Pablo G. Debenedetti
Summary: The separation of substances into different phases is a common and important phenomenon in nature and has scientific and technological significance. When the species involved can interconvert, the presence of a strong external force can result in equal amounts of both alternative species and the observation of steady-state, restricted phase separation. This study uses simulations to investigate the formation of such mesoscale steady-state structures in binary mixtures that exhibit both equilibrium and forced interconversion, and shows that a nonequilibrium thermodynamic theory can explain the main trends and observations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Chemistry, Physical
Pablo M. Piaggi, Roberto Car, Frank H. Stillinger, Pablo G. Debenedetti
Summary: Understanding the behavior of chiral molecules in condensed phase is crucial for biology and various technological applications. In this study, molecular dynamics simulations were used to investigate a chiral molecular model with second-order symmetry-breaking phase transition and determine the critical temperature. The finite-size scaling behavior of the order parameter suggests compatibility with the 3D Ising universality class. The presence of a free energy barrier indicates a suppressed fluctuation between the enantiomers, which could explain the origin of biological homochirality.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Pablo M. Piaggi, Thomas E. Gartner III, Roberto Car, Pablo G. Debenedetti
Summary: The possible existence of a liquid-liquid critical point in deeply supercooled water has been debated. Mishima and Stanley studied the melting curves of different ice polymorphs and suggested that the critical point lies between the melting curves of ice III and ice V. However, our molecular dynamics simulations and machine learning model based on ab initio calculations show that the melting curves of ices III, IV, V, VI, and XIII are supercritical and do not intersect the liquid-liquid transition locus. We conclude that the scenario in which the melting curves are supercritical is favored by the most recent computational and experimental evidence.
JOURNAL OF CHEMICAL PHYSICS
(2023)
