Article
Physics, Fluids & Plasmas
Ivan Kriuchevskyi, Timothy W. Sirk, Alessio Zaccone
Summary: In this study, a mathematical description of amorphous solid deformation and plasticity is presented by extending the concept of instantaneous normal modes (INMs) to deformed systems. The linear response theory is formulated by considering the strain-dependent tangent modulus, and the prediction shows good agreement with simulations.
Article
Biophysics
Yves Dehouck, Ugo Bastolla
Summary: This study investigates the correlation between low-frequency normal modes in elastic network models and large conformational changes in proteins, finding that mode anharmonicity is more strongly related to collectivity than amplitude. Strategies such as reducing degrees of freedom or regularization by torsional harmonic potentials significantly improve the collectivity and harmonicity of normal modes.
BIOPHYSICAL JOURNAL
(2021)
Article
Physics, Fluids & Plasmas
Matteo Baggioli, Alessio Zaccone
Summary: The study derives a theory of specific heat of liquids based on the vibrational density of states, explaining the typical decrease in specific heat with temperature and the correlation between liquid energy barriers and specific heat slopes. The findings demonstrate that the specific heat of liquids is controlled by instantaneous normal modes, providing a missing connection among anharmonicity, saddle points in the energy landscape, and the thermodynamics of liquids.
Article
Chemistry, Physical
Mauricio G. S. Costa, Paulo R. Batista, Antoniel Gomes, Leonardo S. Bastos, Maxime Louet, Nicolas Floquet, Paulo M. Bisch, David Perahia
Summary: MDeNM is an enhanced sampling method that explores conformational changes in proteins with minimal biases. It injects kinetic energy along normal modes describing collective motions. MDexciteR, an automated open-source implementation, integrates MDeNM with commonly used simulation programs with GPU support. This study evaluated the performance and accuracy of the method when using coarse-grained normal modes calculated with elastic network representations, and discussed the advantages and limitations based on test cases.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
Wenjun Zheng
Summary: In order to computationally identify hidden binding sites for allosteric modulators, a fast and simple conformational sampling scheme guided by coarse-grained normal modes solved from the elastic network models followed by atomistic backbone and sidechain reconstruction has been developed. This method can adequately restructure cryptic sites so they are detectable by pocket finding programs like Concavity, making it suitable for high-throughput screening of protein structures at the genome scale. Our method has been used to locate known allosteric sites and predict new promising allosteric sites, and it is both faster and more flexible compared to other sampling methods.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Physics, Multidisciplinary
Norihiro Oyama, Hideyuki Mizuno, Atsushi Ikeda
Summary: This letter reports that the instantaneous normal modes with negative eigenvalues, or so-called imaginary modes, serve as the structural signatures for the Herschel-Bulkley rheology in sheared glasses, providing new insights into the structural origins of the Herschel-Bulkley law.
PHYSICAL REVIEW LETTERS
(2021)
Article
Physics, Fluids & Plasmas
Matteo Baggioli, Alessio Zaccone
Summary: We respond to the Comment by Schirmacher et al. by disagreeing with their claim that the heat capacity of liquids is not a mystery and that there is no evidence for a linear in frequency scaling of the liquid density of states. We emphasize that our theoretical derivation does not assume any Debye density of states and that the Bose-Einstein distribution naturally tends to the Boltzmann distribution in the classical limit. We hope that this scientific exchange will bring more attention to the description of the vibrational density of states and thermodynamics of liquids, which still have many unanswered questions.
Article
Physics, Multidisciplinary
M. Sharif, Amjad Khan
Summary: This paper studies thermal fluctuations, quasi-normal modes and phase transitions of two black holes, and explores their effects on various thermodynamic quantities. It is found that large black holes are stable under thermal fluctuations. The study also establishes a relation between Davies point and quasi-normal modes, and investigates the influence of magnetic charge, correction parameter and dark matter parameter on Hawking temperature and heat capacity.
CHINESE JOURNAL OF PHYSICS
(2022)
Article
Multidisciplinary Sciences
Walter Schirmacher, Taras Bryk, Giancarlo Ruocco
Summary: This study investigates the instantaneous normal mode spectrum of a simulated soft-sphere liquid at different equilibrium temperatures. The findings reveal a sharp maximum near (but not at) lambda = 0 in the spectrum of eigenvalues rho(lambda), which decreases monotonically with |lambda| on both stable and unstable sides. The temperature strongly affects the spectral shape, with asymmetry at low temperatures and symmetry at high temperatures. A mean-field theory for rho(lambda) based on a heterogeneous elasticity model is proposed and shows good agreement with simulation data.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Chemistry, Medicinal
Afrah Khairallah, Caroline J. Ross, Ozlem Tastan Bishop
Summary: Guanosine triphosphate (GTP) cyclohydrolase I (GCH1) is a crucial enzyme involved in the biosynthesis of folate and tetrahydrobiopterin, essential for DNA replication, cell division, and neurotransmitter production. Understanding the intrinsic dynamics and allosteric modulation of GCH1 structure has potential implications for developing new antineuropathic treatments and antimalarial drugs. The study identified key sites regulating the GCH1 enzyme activity and proposed a starting point for drug development targeting neuropathic disorders and malaria.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Biochemistry & Molecular Biology
Ashish Sethi, Shoni Bruell, Tim Ryan, Fei Yan, Mohammad Hossein Tanipour, Yee-Foong Mok, Chris Draper-Joyce, Yogesh Khandokar, Riley D. Metcalfe, Michael D. W. Griffin, Daniel J. Scott, Mohammad Akhter Hossain, Emma J. Petrie, Ross A. D. Bathgate, Paul R. Gooley
Summary: The conserved motif in the C-terminal of the LDLa module is critical for receptor activity in RXFP1 and RXFP2, with different structures adopted in these two receptors suggesting distinct activation mechanisms. This difference in activation mechanisms could be beneficial for drug development targeting these receptors.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Ruo-Xu Gu, Bert L. L. de Groot
Summary: The authors use MD simulations to investigate the effect of dewetting on the function and conformational transition of potassium channels. The results suggest that insufficient hydration obstructs ion permeation and leads to changes in the function and structure of the channels. This conclusion may be applicable to other ion channels as well.
NATURE COMMUNICATIONS
(2023)
Review
Biochemistry & Molecular Biology
Lauren A. Mayse, Liviu Movileanu
Summary: & beta; barrels are widely distributed proteins found in the outer membranes of mitochondria, chloroplasts, and Gram-negative bacteria. These versatile transmembrane proteins serve multiple functions including transportation, receptor activity, enzyme activity, and structural support. Furthermore, they play a role in pore formation. Understanding the voltage-dependent gating characteristics of & beta; barrels is essential in comprehending their functionality. This article reviews the typical features of voltage-dependent gating and highlights recent advancements in understanding the dynamics of closure in these transmembrane proteins.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Rajat Punia, Gaurav Goel
Summary: Lipid membrane remodeling is crucial for cellular processes, and this study proposes a method using Langevin dynamics to predict system properties. The study also explores the impact of different reaction coordinates on pore formation in lipid membranes.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Spectroscopy
E. Benassi, H. Fan
Summary: This study revisited the vibrational normal modes of pyridine, focusing on the in-plane ring motion and analyzing the electronic structure through Quantum Chemical calculations and various dynamic methods. The aim of this investigation is to provide readers with a quantitative characterization of the RNMs of pyridine.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2021)