Review
Physics, Multidisciplinary
Vladimir N. Novikov, Alexei P. Sokolov
Summary: This review focuses on the mechanisms that control the steepness of the temperature dependence of structural relaxation in glass-forming liquids. It discusses the specific case of polymeric glass-forming liquids and the possible role of quantum effects in the glass transition.
Article
Physics, Applied
Julio C. Martinez-Garcia, Rafael Levit, Diego A. Ochoa, Jose E. Garcia
Summary: The fragility parameter, an important material constant in glass science, has been introduced to relaxor ferroelectrics for the first time in this study. By combining a new formulation with experimental data, the researchers successfully elucidated new information about the ferroelectric order in relaxor ferroelectrics. This may lead to a new pathway for understanding relaxation phenomena in other relaxor ferroics.
JOURNAL OF APPLIED PHYSICS
(2021)
Article
Chemistry, Physical
J. C. Yungbluth, G. A. Medvedev, B. M. Savoie, J. M. Caruthers
Summary: This study uses molecular dynamics simulations to find a simple functional relationship between a structural property and the temperature dependent translational diffusion coefficient. The relationship is described by the mean squared-force per molecule, F-2, and holds for various systems and different temperature ranges. This discovery sheds light on the physical mechanisms governing molecular mobility in liquids.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
Ana Vila-Costa, Marta Gonzalez-Silveira, Cristian Rodriguez-Tinoco, Marta Rodriguez-Lopez, Javier Rodriguez-Viejo
Summary: The traditional understanding of the glass transition is challenged by experiments showing that isolated regions of liquid can form within the glassy matrix. The nature of the glass transition depends on the ratio between the relaxation time of the glass and the alpha relaxation time of the equilibrated liquid. At high ratios, high-mobility regions transition directly into the equilibrated liquid, while at low ratios, the glass transition occurs through cooperative relaxation dynamics throughout the material.
Article
Chemistry, Physical
Kimyung Kim, Soohyun Lee, Taegeun Kim, You Kyoung Chung, Joonsuk Huh, Jaesung Yang, Anna Lee, Keewook Paeng
Summary: The rotational dynamics of fluorescent probes of different sizes in glass-forming materials were studied to understand the relationship between time distribution and length scale of dynamic heterogeneity. The results showed that as the probe size increased, the rotation correlation time shifted to longer times, and the length scale associated with the glass transition was estimated. The estimated length scale roughly matched with calorimetric analysis but was smaller than other measurements, showing a decrease in length scale with an increase in the stretching exponent of the system.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Peng Luo, Yanqin Zhai, Peter Falus, Victoria Garcia Sakai, Monika Hartl, Maiko Kofu, Kenji Nakajima, Antonio Faraone, Y. Z
Summary: The relaxation behavior of glass formers at different microscopic length scales exhibits different characteristics, and the length scale dependence is important for understanding the collective relaxation dynamics in glass-forming liquids.
NATURE COMMUNICATIONS
(2022)
Article
Polymer Science
Takashi Sasaki, Yuya Tsuzuki, Tatsuki Nakane
Summary: The article proposes a dynamically correlated network (DCN) model to explain the non-Arrhenius behavior of segmental dynamics in glass-forming liquids, showing that dynamically correlated regions grow during cooling, leading to the viscous slowdown of supercooled liquids. The model suggests that cooperative regions of collective motions have a network structure with string-like parts, and the resulting networks interpenetrate each other, affecting segmental relaxation time and size distribution of the networks.
Article
Chemistry, Physical
Florian Hausen
Summary: Ionic liquids (ILs) have significant applications in lubrication, catalysis, and battery electrolytes. The time required to form a stable interface between ILs and charged surfaces is crucial in many applications. This study demonstrates the probing of ILs' relaxation times using friction force microscopy, showing that the friction force is highly sensitive to even subtle changes in the ILs' interfacial configuration. Various relaxation processes with different time scales are observed, and a significant difference is found depending on the direction of applied potential switching. Furthermore, variations in height after potential steps and the presence of trace amounts of water are discussed.
Article
Multidisciplinary Sciences
Jing Jiang, Zhen Lu, Jie Shen, Takeshi Wada, Hidemi Kato, Mingwei Chen
Summary: The study reveals that high entropy metallic glasses exhibit a depressed dynamical glass transition phenomenon, with HEMGs having moderate calorimetric T-g showing the highest T-alpha and the maximum activation energy of alpha-relaxation. This decoupling of glass transitions from thermal and mechanical measurements demonstrates the impact of high configurational entropy on the structure and dynamics of supercooled liquids and metallic glasses.
NATURE COMMUNICATIONS
(2021)
Article
Physics, Multidisciplinary
Peter Lunkenheimer, Alois Loidl, Birte Riechers, Alessio Zaccone, Konrad Samwer
Summary: The Lindemann criterion applies to the melting of crystals but not to glasses. There is a universal relationship between glass temperature and thermal expansion. The thermal expansion coefficient of glasses behaves differently from crystals, indicating a liquid-solid cross-over in glasses.
Article
Physics, Multidisciplinary
Marian Paluch, Beibei Yao, Jurgen Pionteck, Zaneta Wojnarowska
Summary: One challenging problem in the study of liquid-glass transition phenomenon is to establish a connection between intermolecular interactions and molecular dynamics behavior. By introducing the density scaling concept, significant progress has been made in solving this problem. The relaxation dynamics of different glass formers satisfy an alternative scaling relationship, which can be determined through temperature and pressure evolutions.
PHYSICAL REVIEW LETTERS
(2023)
Article
Physics, Fluids & Plasmas
Vincent E. Debets, Chengjie Luo, Simone Ciarella, Liesbeth M. C. Janssen
Summary: Generalized mode-coupling theory (GMCT) is a promising first-principles theory for studying the dynamics of glass-forming materials, improving predictions by including the exact dynamics of higher-order correlation functions. The study provides a detailed derivation of GMCT for colloidal mixtures obeying a many-body Smoluchowski equation, demonstrating the similarity between Brownian and Newtonian MCT. The theory has been validated through solving generalized mode-coupling equations for a binary Kob-Andersen Lennard-Jones mixture undergoing Brownian dynamics, confirming its improved predictive power.
Review
Chemistry, Physical
Giulio Biroli, Jean-Philippe Bouchaud, Francois Ladieu
Summary: The anomalous growth of the peak value of nonlinear susceptibilities is a signature of growing amorphous order in glassy systems, with spin-glasses as an example. Experimental results on supercooled liquids support the prediction of compact glassites increasing in volume with decreasing temperature or as the system ages, as explained within the random first-order transition (RFOT). The difficulty in explaining this behavior within purely kinetic theories of glass formation is clarified, despite recent claims to the contrary.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Ming Yang, Wenyue Li, Xiongjun Liu, Hui Wang, Yuan Wu, Xianzhen Wang, Fei Zhang, Qiaoshi Zeng, Dong Ma, Haihui Ruan, Zhaoping Lu
Summary: This study demonstrates the significance of configurational entropy (S-conf) in the glass transition process through experimental and simulation results. A higher S-conf leads to a more stable and ordered glass structure.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Simone Ciarella, Chengjie Luo, Vincent E. Debets, Liesbeth M. C. Janssen
Summary: The paper investigates the hierarchical extension of Generalized Mode-Coupling Theory for highly polydisperse materials, which surpasses the predictive power of traditional Mode-Coupling Theory and provides a better understanding of the role of attraction in supercooled liquids.
EUROPEAN PHYSICAL JOURNAL E
(2021)
Article
Chemistry, Physical
Heidi Klem, Glen M. Hocky, Martin McCullagh
Summary: This study introduces a method called shape-GMM which addresses the limitations of using particle positions by employing a weighted maximum likelihood alignment procedure. The alignment strategy is integrated into an expectation maximization Gaussian mixture model (GMM) procedure to identify metastable states. The resulting algorithm can differentiate between various structures, including those that are indistinguishable by root-mean-square displacement and pairwise distances.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Chu Zheng, Yuezhi Mao, Jacek Kozuch, Austin Atsango, Zhe Ji, Thomas E. Markland, Steven G. Boxer
Summary: The electric field orientation can be extracted using a two-directional vibrational probe by exploiting the vibrational Stark effect. Solvents act similarly in stabilizing large bond dipoles at the expense of small ones, regardless of their polarities.
Article
Multidisciplinary Sciences
Bojian Ding, Heidy Y. Narvaez-Ortiz, Yuvraj Singh, Glen M. Hocky, Saikat Chowdhury, Brad J. Nolen
Summary: Arp2/3 complex nucleates branched actin filaments and provides pushing forces for cellular processes. This study reveals the contacts between Arp2/3 complex and the mother actin filament, suggesting that actin filaments stimulate subunit flattening for complex activation. However, limited contact between the bottom half of the complex and the mother filament may explain why actin filaments are required but insufficient to trigger nucleation during WASP-mediated activation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Kenneth A. Jung, Thomas E. Markland
Summary: The third-order response is crucial for simulating and interpreting nonlinear spectroscopies. It can be formulated in terms of equilibrium symmetrized Kubo transformed correlation functions, which provide a practical method for calculating the atomistic dynamics of large condensed phase systems. This approach captures features such as anharmonically induced vertical splittings and peak shifts, and provides a physically transparent framework for understanding multidimensional spectroscopies.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Steven D. E. Fried, Chu Zheng, Yuezhi Mao, Thomas E. Markland, Steven G. Boxer
Summary: The ability to measure and control electric fields in enzymes and other complex reactive environments using the vibrational Stark effect has sparked interest in understanding the role of solute electronic structure in modifying the local solvent organization and electric field. This study demonstrates that amide-containing molecules experience larger frequency shifts in polar solvents compared to non-amide carbonyls due to the stronger p-pi conjugation and larger C=O bond dipole moments, resulting in larger solvent electric fields. The structural modifications of the solute can be used to tune both the solvent organization and electrostatic environment.
JOURNAL OF PHYSICAL CHEMISTRY B
(2022)
Editorial Material
Multidisciplinary Sciences
Pilar Cossio, Glen M. Hocky
Article
Chemistry, Physical
Austin O. Atsango, Andres Montoya-Castillo, Thomas E. Markland
Summary: Linear and nonlinear electronic spectra are important tools to study electronic energy absorption and transfer. A pure state Ehrenfest approach is introduced to accurately calculate these spectra for systems with many excited states and complex chemical environments. By representing the initial conditions as sums of pure states and unfolding multi-time correlation functions, significant improvements in accuracy can be achieved, especially when the initial condition involves coherence between excited states. This method is able to quantitatively capture exact linear, 2D electronic spectroscopy, and pump-probe spectra for various bath regimes.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Michael S. Chen, Joonho Lee, Hong-Zhou Ye, Timothy C. Berkelbach, David R. Reichman, Thomas E. Markland
Summary: This study utilizes recent advances in periodic electronic structure and a transfer learning scheme to obtain machine-learned potential energy surfaces for simulating liquid water. The results reveal the interplay of dynamical electron correlation and nuclear quantum effects across the entire temperature range of liquid water, and provide a strategy for efficiently exploring disordered condensed-phase systems using periodic correlated electronic structure methods.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Multidisciplinary Sciences
Peter Eastman, Pavan Kumar Behara, David L. Dotson, Raimondas Galvelis, John E. Herr, Josh T. Horton, Yuezhi Mao, John D. Chodera, Benjamin P. Pritchard, Yuanqing Wang, Gianni De Fabritiis, Thomas E. Markland
Summary: The SPICE dataset is a new quantum chemistry dataset for training potentials relevant to simulating drug-like small molecules interacting with proteins. It contains over 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It provides both forces and energies calculated at the omega B97M-D3(BJ)/def2-TZVPPD level of theory.
Article
Chemistry, Physical
Andres Montoya-Castillo, Thomas E. Markland
Summary: This paper investigates the dynamics of many-body fermionic systems and derives conditions under which fermionic operators can be replaced by bosonic operators while still capturing the correct dynamics of n-body operators. The analysis provides a guide on how to calculate single- and multi-time correlation functions essential in describing transport and spectroscopy using these simple maps. The applicability of Cartesian maps in capturing correct fermionic dynamics in select models of nanoscopic transport is rigorously analyzed and illustrated with exact simulations of the resonant level model.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Subarna Sasmal, Martin McCullagh, Glen M. Hocky
Summary: In this work, we show that applying Linear Discriminant Analysis (LDA) to atomic positions is an effective way to obtain a good reaction coordinate between two different states of a biomolecule. The lack of rotational and translational invariance has prevented the use of atomic coordinates in enhanced sampling studies. However, by considering molecular configurations as members of equivalence classes in size-and-shape space, we overcome this issue and produce reaction coordinates that effectively characterize the transition between two states and allow for free energy estimation using enhanced sampling MD techniques.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Kenneth A. Jung, Joseph Kelly, Thomas E. Markland
Summary: Electron transfer at electrode interfaces to molecules in solution or at the electrode surface is essential for technological processes, and it necessitates a comprehensive and accurate understanding of the fermionic states of the electrode and their coupling to the molecule being oxidized or reduced in electrochemical processes. A physically transparent quasiclassical scheme is proposed to treat these electron transfer processes in the presence of molecular vibrations, effectively mapping the fermionic variables. This approach accurately captures the electron transfer dynamics even in weak coupling regimes, providing a scalable strategy for treating electron transfer from electrode interfaces in condensed-phase molecular systems.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Austin O. Atsango, Tobias Morawietz, Ondrej Marsalek, Thomas E. Markland
Summary: The transport of excess protons and hydroxide ions in water is crucial for many important chemical and biological processes. Traditional simulation methods are prohibitively expensive for accurately modeling the associated transport mechanisms. In this study, machine-learned potentials (MLPs) are developed to simulate the transport of excess protons and hydroxide ions at a fraction of the cost of traditional methods, while still reproducing the trends observed in ab initio simulations. These simulations provide insights into the role of hypercoordination in the transport mechanism of hydroxide ions and support the asymmetry in diffusion between excess protons and hydroxide ions.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Michael S. Chen, Yuezhi Mao, Andrew Snider, Prachi Gupta, Andres Montoya-Castillo, Tim J. Zuehlsdorff, Christine M. Isborn, Thomas E. Markland
Summary: Hydrogen bonding interactions between chromophores in chemical and biological environments play a crucial role in their electronic absorption and relaxation processes, as evident in their linear and multidimensional optical spectra. However, simulating the large number of atoms in the condensed phase has traditionally limited the use of high-level excited-state electronic structure methods. Utilizing transfer learning, this study demonstrates the construction of machine-learned models to accurately predict the high-level excitation energies of a chromophore in solution using only 400 high-level calculations. Furthermore, by effectively treating the electronic excitations of the green fluorescent protein chromophore in water with EOM-CCSD embedded in a DFT description of the solvent, the optical spectrum is correctly captured, attributing the improvement to the accurate treatment of the coupling of the electronic transition to electric fields, resulting in a stronger response upon hydrogen bonding between the chromophore and water.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Physical
Gaurav Mitra, Chuan Chang, Angus McMullen, Daniela Puchall, Jasna Brujic, Glen M. Hocky
Summary: Colloidal particles with mobile binding molecules allow for spontaneous control over the number of droplet-droplet bonds by tuning the concentration of binders. A coarse-grained molecular dynamics model was used to study the self-assembly of these systems and explore how the valence of assembled structures can be controlled through the kinetics of binding and unbinding. This model provides insights into the molecular features governing valence control and can guide programmable design in experiments.
