Article
Chemistry, Multidisciplinary
Sangmin Lee, Thi Vo, Sharon C. Glotzer
Summary: In this study, hard truncated triangular bipyramids self-assemble into seven different colloidal clathrate crystals, consisting of cages that are either empty or occupied by guest particles. Monte Carlo simulations reveal that the crystallization occurs through the compartmentalization of entropy between low- and high-entropy subsystems for the host and guest particles. The researchers also use entropic bonding theory to design host-guest colloidal clathrates with explicit interparticle attraction for experimental realization.
Article
Multidisciplinary Sciences
Rachael A. Mansbach, Srirupa Chakraborty, Kien Nguyen, David C. Montefiori, Bette Korber, S. Gnanakaran
Summary: The emergence of the G-form variant of COVID-19 has led to a more infectious strain with increased viral loads, likely due to changes in protein energetics favoring infection-capable states and enhanced exposure of the receptor binding domain. These findings are crucial for vaccine design.
Article
Chemistry, Physical
Chang Woo Kim, Ignacio Franco
Summary: This method decomposes the energy dissipation in open quantum systems into contributions due to individual bath components, based on a vibronic extension of the Forster resonance energy transfer theory. Benchmarking against mixed quantum-classical simulations shows that it provides a semi-quantitative frequency-dependent decomposition of the overall dissipation.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Polymer Science
Carlo Andrea Massa, Francesco Puosi, Antonio Tripodo, Dino Leporini
Summary: The vibrational dynamics of a model polymer glass is studied using Molecular Dynamics simulations, focusing on the soft monomers and their tendency to form quasi-local clusters with strong anisotropy in shape. Limited size systems were used to better understand the role of these soft monomers.
Article
Chemistry, Physical
Lea M. Ibele, Basile F. E. Curchod
Summary: Full multiple spawning (FMS) provides an exciting framework for simulating the excited-state dynamics of molecular systems, with ab initio multiple spawning (AIMS) being a recognized method stemming from FMS. AIMS has been successfully used to simulate the nonadiabatic dynamics of numerous complex molecules. The article assesses AIMS performance in describing nonadiabatic dynamics through a conical intersection.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Physics, Fluids & Plasmas
Benjamin Pampel, Simon Holbach, Lisa Hartung, Omar Valsson
Summary: A common problem in computational physics and chemistry is the sampling problem, where high kinetic barriers hinder proper sampling of energy landscapes. To address this problem, many enhanced sampling methods have been developed. In a recent study, the authors introduced a novel sampling algorithm that combines overdamped Langevin dynamics with a birth-death process. In this work, the authors expand on this idea and show that the modified algorithm can efficiently sample rare event energy landscapes, regardless of the barrier height.
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
Energy & Fuels
Bhanu Prakash Sandaka, Jitendra Kumar, Jose Savio Melo
Summary: This study investigated the denaturation of Candida rugosa lipase induced by methanol and the effects of adding glycine betaine (GB) on the catalytic activity of the enzyme in the presence of methanol using molecular dynamics simulations. The results showed that GB can significantly reduce lipase denaturation and maintain its catalytic activity in the presence of methanol.
Article
Chemistry, Physical
Nisha Amarnath Jonniya, Md Fulbabu Sk, Parimal Kar
Summary: The WNK kinase is important in blood pressure regulation, with WNK1 being a potential target for hypertension treatment. Allosteric inhibitors, binding to non-conserved sites, induce structural changes that render the kinase inactive. Understanding these mechanisms may aid in the design of specific inhibitors against WNK1.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2021)
Article
Engineering, Chemical
Rui Cui, Shanlong Li, Chunyang Yu, Yuling Wang, Yongfeng Zhou
Summary: This study used molecular dynamics simulations to investigate the effect of water content and equivalent weight on the diffusion of nitrogen molecules in PFSA hydrated membranes, revealing different behaviors of nitrogen molecules under different conditions, providing a fundamental understanding of nitrogen transport in PFSA hydrated membranes.
JOURNAL OF MEMBRANE SCIENCE
(2022)
Article
Chemistry, Multidisciplinary
Menghao Yang, Yifei Mo
Summary: The text discusses the interface issues between Li metal anode and solid electrolyte in solid-state batteries, revealing the harmful effects of the interfacial defect Li layer on battery performance. It also explores how interfaces with good lattice coherence can reduce Li defects and suppress interface failure.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Thermodynamics
Ben-Xi Zhang, Xin He, Shuo-Lin Wang, Shao-Fei Zheng, Yan-Ru Yang, Xiao-Dong Wang, Duu-Jong Lee
Summary: The phase change behavior of liquid argon nanofilms on gold nanopillar-arrayed surfaces is influenced by factors such as thickness and nanopillar height, with the Wenzel state having a lower onset temperature and being more prone to explosive boiling.
INTERNATIONAL JOURNAL OF THERMAL SCIENCES
(2022)
Article
Chemistry, Physical
D. Aristoff, J. Copperman, G. Simpson, R. J. Webber, D. M. Zuckerman
Summary: The weighted ensemble (WE) method, an enhanced sampling approach, has gained popularity in computational biochemistry due to improved hardware, software, and algorithmic advancements. Recent results have led to greater computational efficiency, particularly through variance reduction approaches for managing trajectories in systems of any dimensionality.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Yves A. Mantz, Yueh-Lin Lee
Summary: In this study, the first examination of the first six cubic LaMnO3 high-index surfaces ((210), (211), (221), (310), (311), and (320)) is conducted. The surface energies of unrelaxed and relaxed surface models are computed to determine their stability. The (210), (320), (211), and (221) surfaces are found to be more stable compared to the low-index (011) and (111) surfaces. Additionally, a phase change is observed in the (310) and (311) surfaces, making it difficult to determine their relaxed surface energies.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Chemistry, Physical
Xiang Huang, Shengluo Ma, Yunwen Wu, Chaoying Wan, C. Y. Zhao, Hong Wang, Shenghong Ju
Summary: In this study, a hybrid framework combining automated physical feature engineering and symbolic regression was proposed for exploring amorphous polymers with desired thermal conductivity. Machine learning models based on optimized descriptors recommended several polymer candidates with good thermal conductivity, and the relationship between macromolecular structure and thermal conductivity was established.
JOURNAL OF MATERIALS CHEMISTRY A
(2023)
Article
Biochemistry & Molecular Biology
Julian A. Harris, Bryan Faust, Arisbel B. Gondin, Marc Andre Damgen, Carl-Mikael Suomivuori, Nicholas A. Veldhuis, Yifan Cheng, Ron O. Dror, David M. Thal, Aashish Manglik
Summary: The neuropeptide substance P activates the neurokinin-1 receptor through interactions deep within the receptor, while interactions between the neuropeptide and the receptor extracellular loops regulate G protein signaling selectivity. This study sheds light on how different stimuli can lead to distinct G protein signaling at the same receptor.
NATURE CHEMICAL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Lucy Kate Ladefoged, Rebekka Koch, Philip C. Biggin, Birgit Schiott
Summary: Studying the action of multimodal antidepressant drug vortioxetine (VXT) on different receptors can provide insights into the mechanisms of agonist-antagonist dual behavior and activation without polar interaction with helix 5.
ACS CHEMICAL NEUROSCIENCE
(2022)
Article
Chemistry, Physical
Zhiyi Wu, Philip C. Biggin
Summary: Absolute binding free-energy calculations play a crucial role in drug design, but accuracy is of utmost importance. This study explores the most suitable approach for simulation boxes containing lipid bilayers, and introduces the Rocklin correction method for lipid bilayer systems.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Harold Grosjean, Mehtap Isik, Anthony Aimon, David Mobley, John Chodera, Frank von Delft, Philip C. Biggin
Summary: A novel crystallographic fragment screening data set was generated and used in the SAMPL7 challenge for protein-ligands. The results show that there is room for improvement in the development of computational tools particularly when applied to fragment-based drug design.
JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
(2022)
Article
Physiology
Adamo S. Mancino, William G. Glass, Yuhao Yan, Philip C. Biggin, Derek Bowie
Summary: Using electrophysiology and molecular dynamics simulations, this study highlights the role of two alternatively spliced residues in the DI S3-S4 linker in channel activation of Nav1.5 and suggests a conserved function in Nav1.4 isoform. Understanding the structural mechanisms of alternative splicing in gating properties of voltage-gated ion channels can provide insights into therapeutic target identification and drug development for related cardiac disorders.
JOURNAL OF GENERAL PHYSIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Tsung-Han Chou, Max Epstein, Kevin Michalski, Eve Fine, Philip C. Biggin, Hiro Furukawa
Summary: Excitatory signaling mediated by N-methyl-d-aspartate receptor (NMDAR) is critical for brain development and function, as well as for neurological diseases and disorders. Channel blockers of NMDARs are of medical interest owing to their potential for treating depression, Alzheimer's disease, and epilepsy. However, precise mechanisms underlying binding and channel blockade have remained limited owing to challenges in obtaining high-resolution structures at the binding site within the transmembrane domains.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(2022)
Review
Physiology
David Seiferth, Philip C. Biggin, Stephen J. Tucker
Summary: This article discusses the hydrophobic gating mechanism in ion channels, which regulates ion permeation by controlling the wetness of the pore. The article provides a detailed definition of hydrophobic gating, compares it with other gating mechanisms, and describes the best practices for identifying a hydrophobic gate.
JOURNAL OF GENERAL PHYSIOLOGY
(2022)
Article
Multidisciplinary Sciences
Arvind Kumar, Kayla Kindig, Shanlin Rao, Afroditi-Maria Zaki, Sandip Basak, Mark S. P. Sansom, Philip C. Biggin, Sudha Chakrapani
Summary: This study reveals the structures of Glycine receptors (GlyRs) bound to Delta 9 -tetrahydrocannabinol (THC) using cryo-electron microscopy, providing insights into the therapeutic effects of cannabinoids.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Multidisciplinary
Irfan Alibay, Aniket Magarkar, Daniel Seeliger, Philip Charles Biggin
Summary: The authors evaluate the use of absolute binding free energy calculations in guiding fragment optimization decisions and find that such calculations can effectively guide fragment elaborations to maximize affinity.
COMMUNICATIONS CHEMISTRY
(2022)
Article
Chemistry, Physical
Simon M. Lichtinger, Philip C. Biggin
Summary: The structure of proteins holds the key to understanding their function, but studying the conformational transitions is challenging. The traditional molecular dynamics simulation suffers from starting-state dependence, while the new MEMENTO method provides a solution.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Multidisciplinary Sciences
Eric Gibbs, Emily Klemm, David Seiferth, Arvind Kumar, Serban L. Ilca, Philip C. Biggin, Sudha Chakrapani
Summary: In this study, cryo-EM structures of the α1βGlyR in the presence of an antagonist, agonist, and agonist with a positive allosteric modulator were determined. The structures revealed distinct pore conformations with varying degrees of asymmetry, and the receptors were found to be in closed or desensitized states. Subunit-specific features and characteristics of the extracellular and intracellular domains were also identified. These findings provide a framework for further investigations into the function of this physiologically important channel.
NATURE COMMUNICATIONS
(2023)
Article
Chemistry, Medicinal
Suleyman Selim Cinaroglu, Philip C. Biggin
Summary: Understanding the thermodynamic signature of protein-peptide binding events is a major challenge in computational chemistry. This study computed the enthalpy of binding for protein-peptide complexes using available experimental data and identified key sampling problems that can be addressed to improve the agreement with experiments. The results show the potential of computational calorimetry in predicting protein-peptide binding enthalpy.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Sueleyman Selim Cinaroglu, Philip C. C. Biggin
Summary: The enthalpic and entropic components of ligand-protein binding free energy are challenging to predict accurately. Recent advances in predicting relative and absolute binding free energies have been successful, but predicting the enthalpic contributions remains challenging. A study evaluating the performance of absolute enthalpy of binding calculations for inhibitors against a bromodomain protein showed good agreement with experimental data and revealed the importance of considering conformational dynamics of a specific loop in improving accuracy.
Article
Chemistry, Physical
David Seiferth, Stephen J. Tucker, Philip C. Biggin
Summary: Transmembrane anion transport by synthetic ionophores is important for understanding endogenous anion transport and has potential therapeutic implications. Computational studies using non-polarizable and polarizable force fields provide insights into the binding properties of anions. The results show solvent dependency and the importance of electrostatics and oxidation status in anion recognition.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2023)
Article
Chemistry, Multidisciplinary
Daniel Crusius, Jason R. Schnell, Flaviu Cipcigan, Philip C. Biggin
Summary: Knowing the solution structures of cyclic peptides is crucial for predicting the pharmacokinetic properties in drug discovery. In this study, we introduced the MacroConf dataset and computational workflows to evaluate the performance of current in silico methods in reproducing experimental cyclic peptide solution structures. Our findings show that enhanced sampling molecular dynamics methods, like Gaussian accelerated MD, performed well in reproducing experimental results. Conventional MD suffered from limited sampling, especially for compounds with proline isomerization. Cheminformatics-based conformer generators generated diverse and plausible structures that matched the sampling observed in MD-based methods, but did not provide thermodynamic insights. The presented computational workflow can be easily extended to include new compounds or different simulation methods, serving as a benchmark to improve cyclic peptide conformer generators.
