Article
Mathematics, Applied
Jacques Fejoz, Andreas Knauf, Richard Montgomery
Summary: The text discusses the scattering of n classical particles interacting via pair potentials, focusing on the 'free region' where well-defined and well-separated final states at infinity can be achieved. It proves the existence of a global surface of section for the free region, establishing a smooth map between a point and its final state, and a forward conjugacy between n-body dynamics and free dynamics.
Article
Chemistry, Physical
Ryo Kawada, Katsuhiro Endo, Daisuke Yuhara, Kenji Yasuoka
Summary: Molecular dynamics simulation is a method for studying the behavior of molecules, but its high computational cost has always been a problem. MD-GAN is a machine learning-based method that accelerates the generation of molecular dynamics data. This study explores the effectiveness of incorporating information from other particles in the training process and successfully predicts molecular diffusion.
Article
Biochemistry & Molecular Biology
Till El Harrar, Benedikt Frieg, Mehdi D. Davari, Karl-Erich Jaeger, Ulrich Schwaneberg, Holger Gohlke
Summary: This study investigates the impact of aqueous ionic liquids on a model enzyme through molecular dynamics simulations and finds that they can affect enzyme activity by modifying local structural stability, eventually leading to perturbations in the catalytic site and protein core. The identification of perturbation pathways and specific interactions with IL ions helps predict variant libraries with improved tolerance to aqueous ionic liquids.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Physical
Joshua T. Berryman, Amirhossein Taghavi, Florian Mazur, Alexandre Tkatchenko
Summary: To improve the accuracy of molecular dynamics simulations, classical forcefields are supplemented with a kernel-based machine learning method trained on quantum-mechanical fragment energies. The study finds that classical DNA models have excessive stiffness when it comes to stretching, which is not confirmed by experimental studies. Quantum correction provides a better explanation for the discrepancy between single molecule stretching experiments and classical calculations of DNA stretching. This research is important for nucleic acid simulations and biomolecular simulations in general.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Diandong Tang, Luyang Jia, Lin Shen, Wei-Hai Fang
Summary: In this study, the researchers utilized long short-term memory (LSTM) networks to accelerate the time evolution of the electronic subsystem in photophysics and photochemistry. By constructing networks, generating trajectory ensembles, and simulating the mechanism of nonadiabatic processes, they successfully reproduced Tully's three models.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
John Strahan, Adam Antoszewski, Chatipat Lorpaiboon, Bodhi P. Vani, Jonathan Weare, Aaron R. Dinner
Summary: This study introduces a new dynamical approximation method, the dynamical Galerkin approximation, to reduce dependence on lag time selection and provide improved estimators for rates and committors. Simple procedures are also proposed for constructing suitable smoothly varying basis functions from arbitrary molecular features, and these methods are evaluated using a dataset.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Biochemistry & Molecular Biology
Dorota Kowalska, Joanna Dolzonek, Krzysztof Zamojc, Sergey A. Samsonov, Martyna Maszota-Zieleniak, Joanna Makowska, Piotr Stepnowski, Anna Bialk-Bielinska, Dariusz Wyrzykowski
Summary: Human serum albumin (HSA) plays a crucial role in binding low-molecular-weight compounds and facilitating their distribution in living organisms. This study investigates the impact of counter-ions, such as [B (CN)4]- and [C(CN)3]-, on the affinity of [IM1-12]+ towards HSA. Experimental methods and computational approaches are used to analyze protein-ligand interactions and the thermal stability of resulting complexes. The findings provide valuable insights into the presence of globular proteins and ionogenic compounds in the environment and living organisms.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Article
Biochemistry & Molecular Biology
Emily Agnello, Joshua Pajak, Xingchen Liu, Brian A. Kelch
Summary: In this study, a molecular model for the tail tube assembly of long-tailed bacteriophages is proposed, based on high-resolution cryo-EM structures of the P74-26 phage. The results reveal that the P74-26 phage assembles through tight ball-and-socket-like interactions between flexible loops and neighboring rings. A model for the assembly of conserved tube-like structures across phage and other entities possessing tail tube-like proteins is proposed, which is supported by mutational, light scattering, and molecular dynamics simulations data. The cooperative interaction of dynamic intraring and interring contacts controls tail assembly, leading to the high-fidelity assembly of long, stable tubes.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Physical
Shreyas Malpathak, Nandini Ananth
Summary: The mixed quantum classical (MQC)-initial value representation (IVR) is a semiclassical framework that selectively quantizes the modes of a complex system. It accurately reproduces nuclear quantum coherences and conserves zero-point energy in the quantum limit, but is less accurate in the classical limit. By modifying the MQC approach, we show analytically that it is exact for all correlation functions at time zero and numerically demonstrate its correctness in capturing the quantum and classical limits of zero-point energy (ZPE) flow. Interestingly, selective quantization of the system allows for prediction and modification of ZPE flow direction.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Fluids & Plasmas
Philipp Stroeker, Karsten Meier
Summary: In this study, molecular expressions for thermodynamic properties and derivatives of the entropy up to third order in the adiabatic grand-isochoric & μVL and adiabatic grand-isobaric & μpR ensembles were systematically derived. These expressions are represented by phase-space functions, which correspond to the derivatives of the entropy with respect to the chemical potential, volume, and Hill energy L in the μVL ensemble, or with respect to the chemical potential, pressure, and Ray energy R in the μpR ensemble. The derived expressions were validated through Monte Carlo simulations using the Lennard-Jones model fluid at three selected state points.
Article
Chemistry, Physical
G. De Thomasis, A. Galante, G. Fioravanti, L. Ottaviano, M. Alecci, G. Profeta
Summary: We calculate the spin-lattice relaxation time of water in contact with graphene oxide using molecular dynamics simulations. The water-graphene oxide interaction is characterized by calculating the relaxation properties of bulk water and the contact angle, and comparing them with experimental data. The effect of graphene oxide on the dynamics and relaxation properties of water in different conditions and concentrations is investigated. Despite the diamagnetic nature of graphene oxide, the confined bilayers strongly affect the longitudinal relaxation properties of interfacial water due to hydrogen bonds with oxygen groups, making it a promising platform for studying water dynamics in confined geometries and a potential contrast-agent for MRI applications.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Dhiman Ray, Sharon Emily Stone, Ioan Andricioaei
Summary: The Markovian Weighted Ensemble Milestoning (M-WEM) introduces a scheme for efficiently calculating thermodynamic and kinetic properties of biomolecular processes. It has been tested on various models and systems, demonstrating high accuracy and low computational cost, making it a potential tool for computational drug design.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Multidisciplinary Sciences
N. Gao, Z. W. Yao, G. H. Lu, H. Q. Deng, F. Gao
Summary: The study found a new diffusion mechanism for <100> interstitial dislocation loops in BCC iron using self-adaptive accelerated molecular dynamics, which represents a significant step towards understanding the mechanical behavior and microstructure evolution of the material.
NATURE COMMUNICATIONS
(2021)
Article
Chemistry, Physical
Stanly Paul, Swathi Nadendla, M. Elizabeth Sobhia
Summary: The emergence of distinct variants has turned the COVID-19 pandemic into a global health challenge. Omicron, a new variant, has been classified as a variant of concern by the World Health Organization due to its higher mutation rate and accelerated human infection. Inhibition of the interaction between the receptor binding domain (RBD) and the human angiotensin converting enzyme-2 (ACE(2human)) receptor has been proven effective in inhibiting viral infection. Through molecular dynamics simulation, our study explores the atomic details and events of RBD-ACE(2human) interactions, providing insights for the development of therapeutic peptidomimetics targeting omicron.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Shao-Chun Lee, Yanqin Zhai, Zhixia Li, Nathan P. Walter, Melissa Rose, Brent J. Heuser, Yang Zhang
Summary: Researchers developed a neural network force field and a reparametrized rigid ion model to predict the physicochemical properties of molten salts, showing that the neural network force field can accurately reproduce the structural and transport properties of molten salts with computational efficiency.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)