Article
Chemistry, Multidisciplinary
Junais Habeeb Mokkath, Mufasila Mumthaz Muhammed, Ali J. Chamkha
Summary: In this study, Metadynamics simulations were used to investigate the diffusion of vacancies on different Al surfaces. The results showed that each surface exhibited unique characteristics in terms of vacancy diffusion, providing valuable insights for understanding surface vacancy diffusion on technologically relevant Al surfaces.
Article
Multidisciplinary Sciences
Amruthesh Thirumalaiswamy, Robert A. Riggleman, John C. Crocker
Summary: This study reports a modified metadynamics algorithm that efficiently explores and samples low-energy regions of high-dimensional energy landscapes in glass-forming systems. The algorithm successfully discovers and descends meandering canyons in the landscape, allowing for high densities and low energies to be reached.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Physical
Michele Invernizzi, Michele Parrinello
Summary: In adaptive-bias enhanced sampling methods, a bias potential is added to drive transitions between metastable states. There is a tradeoff between exploration and convergence when the collective variables are suboptimal. The OPES method focuses on fast convergence, but a new variant emphasizes quickly escaping metastable states.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Eli Pollak, Salvador Miret-Artes
Summary: In this review, we summarize the recent developments in Kramers' theory of reaction rates. We emphasize the importance of this theory in chemical reactions and discuss the main theoretical formalism based on the generalized Langevin equation and the modern Pollak, Grabert and Hanggi theory. The applications of Kramers' theory in quantum and classical surface diffusion are outlined, and recent applications in various fields such as nanoparticle levitation, microcavity polariton dynamics, and reaction simulation in liquids are presented. The open problems and future challenges of Kramers turnover theory are also discussed.
Article
Chemistry, Analytical
Ryan Muddiman, Kevin O'Dwyer, Charles H. Camp Jr, Bryan Hennelly
Summary: Broadband coherent anti-Stokes Raman scattering (BCARS) can generate high-quality Raman spectra across a wide bandwidth (400-4000 cm(-1)) in milliseconds. However, raw BCARS spectra consist of vibrationally resonant (Raman) and non-resonant (electronic) components, which may pose challenges for chemical analyses. A deep convolutional autoencoder network trained on simulated BCARS-Raman datasets has been developed to extract the Raman signal under ideal conditions. This study introduces a new computational system that combines experimental measurements of laser system properties with simulated susceptibilities, enabling accurate mapping between susceptibility and measured response for a specific BCARS system.
ANALYTICAL METHODS
(2023)
Article
Chemistry, Applied
Manyi Yang, Luigi Bonati, Daniela Polino, Michele Parrinello
Summary: The study of chemical reactions in aqueous media is crucial and challenging due to the involvement of water molecules. Ab-initio molecular dynamics and machine learning potentials offer solutions to model these reactions, but their application is limited by computational cost. In this study, an active learning procedure accelerated by enhanced sampling was used to build a neural-network potential for studying the urea decomposition process in water. The obtained free energy profiles improved the accuracy of kinetic rates calculations, and the formation of the zwitterionic intermediate was found equally probable via an acidic or a basic pathway.
Article
Biochemistry & Molecular Biology
Jigneshkumar Dahyabhai Prajapati, Jose N. Onuchic, Karissa Y. Sanbonmatsu
Summary: The authors introduced a method based on molecular dynamics simulation and metadynamics to study the conformational dynamics of RNA. They developed a collective variable to probe the formation and breakage of tertiary contacts in RNA, in order to reveal the free energy landscape. The method was validated through its application in the SAM-I riboswitch.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Chen Ye, Suman Mallick, Manuel Hertzog, Markus Kowalewski, Karl Borjesson
Summary: Strong light-matter coupling can modify the molecular potential energy landscape, providing a wide range of applications for manipulating molecular properties; the research shows that energy can relax directly from molecular states to hybrid light-matter states, laying the groundwork for tunable photon upconversion systems.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Multidisciplinary Sciences
Alexis N. Guidi, Michael E. Mitchell, Jonathan F. Holzman
Summary: In this work, we introduce apertured THz microjets to overcome the fundamental limits of spatial resolution and spectral bandwidth in broadband terahertz (THz) spectroscopy on a subwavelength scale. The coupling through subwavelength apertures enables effective transmission of THz power through samples with broad spectral bandwidths and fine spatial resolutions. Our findings show promise for studying carcinogenesis, pathogenesis, and related areas.
SCIENTIFIC REPORTS
(2023)
Article
Chemistry, Physical
Jakub Rydzewski, Omar Valsson
Summary: The study introduces a new method called MRSE, which utilizes deep neural networks to learn CVs that map high-dimensional feature space to low-dimensional latent space, making it suitable for enhanced sampling simulations.
JOURNAL OF PHYSICAL CHEMISTRY A
(2021)
Article
Chemistry, Physical
Andreas Hulm, Johannes C. B. Dietschreit, Christian Ochsenfeld
Summary: The eABF method and its newer variants enable rapid exploration of the configuration space of chemical systems. By using the MBAR method, statistical weights of individual frames can be computed, enhancing the prediction of nuclear magnetic resonance shieldings for ensemble property calculations.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Review
Chemistry, Multidisciplinary
Neha, Vikas Tiwari, Soumya Mondal, Nisha Kumari, Tarak Karmakar
Summary: Crystallization is an important process in material science, biology, and the environment. Experimental methods provide limited information about crystal formation, while computer simulations can provide microscopic details. Enhanced sampling simulations can overcome the limitations of traditional simulations. This review provides an overview of collective variables (CVs) that have been developed and used for studying crystallization, and discusses the challenges and future directions in developing effective CVs.
Article
Chemistry, Medicinal
Shubhandra Tripathi, Nisanth N. Nair
Summary: Modeling ligand unbinding in proteins for binding free energy estimation and mechanism exploration is challenging due to entropic bottlenecks caused by protein and solvent conformations. Enhanced sampling techniques require very long simulations to sample all conformational states, as the system gets trapped in local free energy minima along transverse coordinates. This study demonstrates that temperature accelerated sliced sampling (TASS) is an ideal approach to overcome difficulties faced by conventional sampling methods in studying ligand unbinding. TASS is used to study the unbinding of avibactam inhibitor molecules from the Class C β-lactamase (CBL) active site, and the simulations successfully extract CBL-avibactam unbinding free energetics, unbinding pathways, and critical interactions.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Physical
Satoru Fukuhara, Kristof M. Bal, Erik C. Neyts, Yasushi Shibuta
Summary: Advanced molecular dynamics simulations and metadynamics simulations were used to construct the free energy surface for carbon segregation in nickel nanoparticles, revealing the relative stability of different stages and the free energy barriers and rates of individual steps. With an increase in carbon concentration, segregated carbon becomes more stable in terms of both enthalpy and entropy.
Article
Plant Sciences
Xian Xiao, Zhiyuan Ma, Jiabao Zhang, Bo Sun, Jizhong Zhou, Yuting Liang
Summary: There is an urgent need to understand the coupled relationship between belowground microbes and aboveground plants in response to temperature under climate change. The metabolic theory of ecology (MTE) provides a way to predict the metabolic rate and species diversity, but the spatial scale dependence and connections between plants and microorganisms are still unclear. This study used two independent datasets to address this question, and found that the spatial turnover of bacterial communities and microbial functional genes increased with temperature and fitted MTE. Through meta-analysis, this temperature-dependent spatial pattern was further extended to the global scale, indicating a close linkage between belowground microorganisms and aboveground plants.