Article
Pharmacology & Pharmacy
Adrian Krummnow, Andreas Danzer, Kristin Voges, Stefanie Dohrn, Samuel O. Kyeremateng, Matthias Degenhardt, Gabriele Sadowski
Summary: This study provides a thermodynamic analysis of the release mechanism of amorphous solid dispersions (ASDs) composed of ritonavir and poly(vinylpyrrolidone-co-vinyl acetate). The observed release behavior is explained based on the quantitative thermodynamic phase diagram predicted by PC-SAFT. Liquid-liquid phase separation in the dissolution medium and amorphous phase separation in the ASD are linked back to the same thermodynamic origin, and they occur simultaneously in the investigated system.
Review
Biochemistry & Molecular Biology
Xiping Gong, Yumeng Zhang, Jianhan Chen
Summary: This paper provides an in-depth review of recent advances in multi-scale simulation of disordered protein states, with a particular emphasis on the development and application of advanced sampling techniques for studying IDPs.
Article
Chemistry, Multidisciplinary
Paul R. Wrona, Eran Rabani, Phillip L. Geissler
Summary: Long-lived indirect excitons exhibit a rich phase diagram, including a Bose-Einstein condensate and a classical liquid state. This study uses theoretical tools to uncover the nature of the condensed phase, attributing it to a quantum electron-hole liquid.
Article
Biochemistry & Molecular Biology
Akie Kowaguchi, Paul E. Brumby, Kenji Yasuoka
Summary: This work demonstrates the advantages of using the temperature and pressure replica-exchange method to investigate phase transitions and hysteresis in liquid-crystal fluids. By applying this method to the Hess-Su liquid-crystal model, heat capacity peaks and phase co-existence points were observed, and the identity of the crystalline phase was determined. It highlights the importance of caution when simulating meta-stable nematic states at higher densities in this system.
Article
Chemistry, Multidisciplinary
Sijie Guo, Yutao Li, Bing Li, Nicholas S. Grundish, An-Min Cao, Yong-Gang Sun, Yan-Song Xu, Yanglimin Ji, Yan Qiao, Qinghua Zhang, Fan-Qi Meng, Zhi-Hao Zhao, Dong Wang, Xing Zhang, Lin Gu, Xiqian Yu, Li-Jun Wan
Summary: This study demonstrates an easy and low-cost wet-chemistry process to engineer the anode/solid electrolyte interface in solid-state batteries (SSBs) with nanoscale precision. By using this strategy, the interfacial resistance between the electrodes and solid-state electrolyte is significantly decreased, leading to improved performance metrics and long cycle life for the SSBs.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2022)
Article
Chemistry, Multidisciplinary
Jun-Chao Liu, Yong Ai, Qin Liu, Yi-Piao Zeng, Xiao-Gang Chen, Hui-Peng Lv, Ren-Gen Xiong, Wei-Qiang Liao
Summary: This article presents a solid-liquid crystal biphasic ferroelectric material, cholestanyl 4-X-benzoate (4X-CB, X = Cl, Br, and I), that exhibits biferroelectricity in both the solid and liquid crystal phases. The liquid crystal phase of 4X-CB is identified as a cholesteric phase with a helical structure, different from the ordinary chiral smectic ferroelectric liquid crystal phase. Furthermore, the spontaneous polarization of 4X-CB in both phases can be regulated by different halogen substitutions. It is suggested that 4X-CB is the first ferroelectric material with tunable biferroelectricity, providing a feasible case for the performance optimization of solid-liquid crystal biphasic ferroelectrics.
ADVANCED MATERIALS
(2023)
Article
Multidisciplinary Sciences
Thomas Linker, Ken-ichi Nomura, Anikeya Aditya, Shogo Fukshima, Rajiv K. Kalia, Aravind Krishnamoorthy, Aiichiro Nakano, Pankaj Rajak, Kohei Shimmura, Fuyuki Shimojo, Priya Vashishta
Summary: This study employs multiscale quantum simulations and machine learning to reveal the polarization control mechanism and topological dynamics change of ferroelectric materials under optical excitation. This research is of great significance for ferroelectric topotronics and optoelectronic applications.
Article
Chemistry, Multidisciplinary
Sagun Jonchhe, Wei Pan, Pravin Pokhrel, Hanbin Mao
Summary: This study found that in Tau protein condensates, the halftime of the liquid-to-solid transition is affected by anions' solvation energy according to the Hofmeister series. Charged groups facilitate the transition, similar to the Hofmeister effect, while hydrophobic alkyl chains and aromatic rings inhibit it. These findings not only elucidate the driving force of the liquid-to-solid transition in Tau condensates but also provide guidelines for designing small molecules to modulate this important transition.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Chemistry, Physical
Sridip Parui, Biman Jana
Summary: The study examines the effect of cold temperature on the alpha-helical region of the Trp-cage miniprotein using molecular dynamics simulations, observing a helix-to-helix transition below 230K primarily driven by water-water interactions. This transition may lead to cold denaturation of the protein. Unlike Trp-cage, the antifreeze protein AFP has a helical arrangement that facilitates hydrogen bonding with surrounding ice-like water molecules, crucial for its antifreeze activity.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Multidisciplinary Sciences
Thomas E. I. I. I. I. I. I. Gartner, Salvatore Torquato, Roberto Car, Pablo G. Debenedetti
Summary: By conducting molecular dynamics simulations, researchers have identified striking characteristics of the liquid-liquid critical point in the glass structure of water, suggesting a surprising relationship between this critical point and the non-equilibrium structure of glassy water. The water-like systems show a strong pressure dependence during vitrification, while simple liquids do not exhibit this behavior.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Multidisciplinary
Meenakshi Sharma, Manju Singh, Rajib K. Rakshit, Surinder P. Singh, Matteo Fretto, Natascia De Leo, Andrea Perali, Nicola Pinto
Summary: Superconducting nanofilms have the ability to transition from 3D to 2D and exhibit Berezinskii-Kosterlitz-Thouless (BKT) superconducting behavior. Further reduction in dimensionality to quasi-1D superconducting nanostructures with disorder can generate quantum and thermal phase slips (PS). The study characterizes superconducting NbN nanofilms of different thicknesses and substrates and observes clear features related to BKT transition and PS events. The analysis suggests that these complex phase phenomena are strongly influenced by the nano-conducting paths and superconducting coherence length.
Article
Physics, Multidisciplinary
Md. S. Hossain, M. K. Ma, K. A. Villegas-Rosales, Y. J. Chung, L. N. Pfeiffer, K. W. West, K. W. Baldwin, M. Shayegan
Summary: The interplay between the Fermi sea anisotropy, electron-electron interaction, and localization phenomena can give rise to exotic many-body phases. This study reports the observation of an ordered anisotropic Wigner solid in a clean two-dimensional electron system with anisotropic effective mass and Fermi sea.
PHYSICAL REVIEW LETTERS
(2022)
Article
Physics, Multidisciplinary
Bing Li, Yang Ding, Duck Young Kim, Lin Wang, Tsu-Chien Weng, Wenge Yang, Zhenhai Yu, Cheng Ji, Junyue Wang, Jinfu Shu, Jiuhua Chen, Ke Yang, Yuming Xiao, Paul Chow, Guoyin Shen, Wendy L. Mao, Ho-Kwang Mao
Summary: The study utilized high-energy synchrotron radiation to investigate the electronic band properties of hydrogen under high pressure in a diamond-anvil cell, finding that the electronic band gap of hydrogen decreased linearly at 90 GPa pressure, with a density increase of 8.6 times.
PHYSICAL REVIEW LETTERS
(2021)
Article
Environmental Sciences
Elmar C. Fuchs, Jakob Woisetschlaeger, Adam D. Wexler, Rene Pecnik, Giuseppe Vitiello
Summary: A horizontal electrohydrodynamic (EHD) liquid bridge, also known as a floating water bridge, forms when high voltage DC is applied to pure water in two separate beakers. The bridge acts as a cylindrical lens that refracts light and can split light into horizontally and vertically polarized components. Resonance effects between the power supply and vortical structures cause waviness at the onset of the bridge, and spikes with increased refractive index are observed moving through it.
Review
Cell Biology
Yuxuan Li, Taoyu Chen, Kaiqing You, Tao Peng, Tingting Li
Summary: Life is composed of functional biomolecules, such as proteins and nucleic acids, which can undergo liquid-liquid phase separation to form liquid droplets. These droplets can transition into solid-like biomolecular condensates, which exist in physiological and pathological conditions. The formation of solid-like condensates, also known as detergent-insoluble aggregates, is not fully understood. Recent research has shown that the transition from a liquid to solid phase is crucial for the formation of these condensates. This review summarizes the sequence regions and solution conditions that impact the phase transition, as well as the methods used to study solid phase components.
AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY
(2023)
Article
Chemistry, Physical
Wenwen Diao, Shengheng Yan, James D. Farrell, Binju Wang, Fangfu Ye, Zhanfeng Wang
Summary: In this study, a revised catalytic mechanism of Uracil-DNA glycosylase (UDG) was proposed, and the nature of its strong catalytic efficiency was elucidated using quantum-mechanical/molecular-mechanical calculations, molecular dynamics simulations, and QM calculations. The study revealed the important role of the internal electric field in different stages of the reaction, and the balance between the catalytic effect of substrate phosphate groups and the counterbalancing effect of sodium ions in the internal electric field. Additionally, the specific roles of Asp145 and His148, as well as their contributions driven by the internal electric field, were identified.
Article
Chemistry, Physical
Guowei Qi, Michail D. Vrettas, Carmen Biancaniello, Maximo Sanz-Hernandez, Conor T. Cafolla, John W. R. Morgan, Yifei Wang, Alfonso De Simone, David J. Wales
Summary: Recent advances in biomolecular simulation and global optimization have utilized hybrid restraint potentials to improve the performance and accuracy of various computational methods. These hybrid potentials combine harmonic restraints with molecular mechanics force fields and have shown promising results in molecular dynamics simulations and structure prediction.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Sabine C. Matysik, David J. Wales, Stephen J. Jenkins
Summary: Adsorption of chiral molecules on chiral surfaces leads to diastereomerism, resulting in different adsorption geometries. Through first-principles molecular dynamics simulations, we demonstrate that this diastereomerism is reflected in the desorption motion of chiral molecules from a chiral surface. When desorbing from R-Cu{531}, S-Ala molecules show larger angular momentum and a preference for one rotational direction, while R-Ala molecules do not exhibit such preference. These trends are reversed for desorption from S-Cu{531}. Potential applications include chiral separation techniques and enantiospecific sensors.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Meng Liu, James D. Farrell, Xianren Zhang, Jure Dobnikar, Stefano Angioletti-Uberti
Summary: We propose a classical density functional theory model to study the self-assembly of polymeric surfactants on curved surfaces. Phase separation driven by size alone is thermodynamically unfavorable on cylindrical and spherical surfaces. By coupling surface topography and polymeric surfactants, non-uniform patterns can be designed on surfaces.
Article
Chemistry, Multidisciplinary
Appan Roychoudhury, Rosalind J. Allen, Tine Curk, James Farrell, Gina McAllister, Kate Templeton, Till T. Bachmann
Summary: The study presents the development of EIS-based biosensors using multivalent binding for sensitive detection of SARS-CoV-2 RNA. The strategy of multivalent binding was found to enhance biosensor performance, with shorter probes demonstrating the best performance in binding with SARS-CoV-2 RNA.
Article
Chemistry, Physical
Boy Choy, David J. Wales
Summary: Rapid advances in quantum computing have provided new opportunities for solving the central electronic structure problem in computational chemistry. In the noisy intermediate-scale quantum (NISQ) era, it is important to use quantum algorithms with short quantum circuits to maximize qubit efficiency. The construction of hardware efficient ansa''tze offers a potential solution, but increasing circuit depth to improve accuracy may result in an abundance of local minima that hinder global optimization. To investigate this phenomenon, we explore the energy landscapes of hardware-efficient circuits and propose a dimensionality reduction procedure that simplifies the energy landscape, speeds up optimization, and retains accuracy for the global minimum from both software and hardware perspectives.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Physics, Multidisciplinary
James Daniel Farrell, Jure Dobnikar, Rudolf Podgornik
Summary: The stability of RNA viruses is influenced by genome topology and the interactions between RNA and capsid proteins. Through modeling, the genome topology is encoded as a graph, with adjacent packaging signals mapped to edges. Through simulations and evaluation of osmotic pressure, it is found that virion stability is dependent on both genome topology and degree of confinement. It is predicted that MS2 bacteriophage would prefer a more linear genome topology.
PHYSICAL REVIEW RESEARCH
(2023)
Article
Chemistry, Physical
David J. Wales
Summary: This paper investigates the multifunnel energy landscapes in multifunctional systems, such as molecular switches. The multifunnel organization is decoded from dynamical signatures in the first passage time distribution between reactants and products. Extracting the corresponding dynamical signatures provides direct insight into the organization of the molecular energy landscape, enabling a rational design of target functionality.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Physics, Fluids & Plasmas
Rebecca A. Bone, Daniel J. Sharpe, David J. Wales, Jason R. Green
Summary: In this article, the authors test the relationship between speed and dissipation for stochastic paths far from equilibrium. By proposing a minimal model for a driven system, the authors find that faster processes can dissipate less under far-from-equilibrium conditions due to strong currents.
Article
Multidisciplinary Sciences
Greg Ashton, Noam Bernstein, Johannes Buchner, Xi Chen, Gabor Csanyi, Andrew Fowlie, Farhan Feroz, Matthew Griffiths, Will Handley, Michael Habeck, Edward Higson, Michael Hobson, Anthony Lasenby, David Parkinson, Livia B. Partay, Matthew Pitkin, Doris Schneider, Joshua S. Speagle, Leah South, John Veitch, Philipp Wacker, David J. Wales, David Yallup
Summary: This Primer examines Skilling's nested sampling algorithm and its application in Bayesian inference and multidimensional integration. The principles of nested sampling are summarized and recent developments using efficient nested sampling algorithms in high dimensions are surveyed. Detailed examples from cosmology, gravitational-wave astronomy, and materials science are provided. Finally, the Primer includes recommendations for best practices and a discussion of potential limitations and optimizations of nested sampling.
NATURE REVIEWS METHODS PRIMERS
(2022)
Correction
Multidisciplinary Sciences
Greg Ashton, Noam Bernstein, Johannes Buchner, Xi Chen, Gabor Csanyi, Andrew Fowlie, Farhan Feroz, Matthew Griffiths, Will Handley, Michael Habeck, Edward Higson, Michael Hobson, Anthony Lasenby, David Parkinson, Livia B. Partay, Matthew Pitkin, Doris Schneider, Joshua S. Speagle, Leah South, John Veitch, Philipp Wacker, David J. Wales, David Yallup
NATURE REVIEWS METHODS PRIMERS
(2022)
Article
Chemistry, Multidisciplinary
Istvan Horvath, David J. Wales, Szilard N. Fejer
Summary: Palladium ions complexed with nonlinear bidentate ligands can form hollow spherical shells. By using model anisotropic mesoscale building blocks, we can reproduce these structures and identify highly cooperative transitions between different polyhedral structures. The curvature of the ligand particles determines the preferred curvature of the building blocks.
NANOSCALE ADVANCES
(2022)
Article
Computer Science, Artificial Intelligence
Maximilian P. Niroomand, John W. R. Morgan, Conor T. Cafolla, David J. Wales
Summary: Minima of the loss function landscape in a neural network are locally optimal sets of weights that specialize in different aspects of a learning problem and process input information differently. By combining the predictive power from multiple minima using a meta-network, a better classifier can be produced, leading to improved performance for complex learning problems. Analyzing symmetry-equivalent solutions also provides a means to enhance the efficiency of this approach.
MACHINE LEARNING-SCIENCE AND TECHNOLOGY
(2022)
Article
Chemistry, Physical
Atreyee Banerjee, Mauricio Sevilla, Joseph F. Rudzinski, Robinson Cortes-Huerto
Summary: We computed partial structure factors, Kirkwood-Buff integrals (KBIs), and chemical potentials of model supercooled liquids with and without attractive interactions. Our results show that attractive interactions favor the nucleation of long-range structures and significantly influence the thermodynamic properties. At higher density, the two systems exhibit similar thermodynamic properties.
Article
Computer Science, Artificial Intelligence
Maximilian P. Niroomand, Conor T. Cafolla, John W. R. Morgan, David J. Wales
Summary: This paper compares the use of cross-entropy loss and direct optimization of AUC for evaluating neural network classifiers. It analyzes the characteristics of approximate AUC loss functions and provides a theoretical explanation. The research findings show that the approximate AUC loss function can improve testing AUC, but its minima are less stable.
MACHINE LEARNING-SCIENCE AND TECHNOLOGY
(2022)
