Article
Chemistry, Physical
Aleksander E. P. Durumeric, Gregory A. Voth
Summary: Bottom-up CG molecular dynamics models, parameterized using complex effective Hamiltonians, are often optimized to approximate high dimensional data from atomistic simulations. However, human validation of these models may not differentiate between the CG model and the atomistic simulations. We propose using classification to estimate high dimensional errors and utilizing explainable machine learning to convey this information to scientists. This approach is demonstrated using Shapley additive explanations and two CG protein models, and may be valuable for assessing the accuracy of allosteric effects in CG models at the atomistic level.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Valery Lutsyk, Pawel Wolski, Wojciech Plazinski
Summary: This article presents a coarse-grained force field dedicated to glucopyranose-based carbohydrates, compatible with the Martini force field. The new model successfully displays spontaneous formation of aggregates with experimentally identified features and accurately identifies binding pockets in carbohydrate-binding proteins.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Amy Clarke, Klaus Groschner, Thomas Stockner
Summary: Through molecular dynamics simulations, we reveal the interaction between cholesterol and multiple elements of the transmembrane machinery of TRPC3 channel, identifying binding sites for cholesterol and its potential role in stabilizing the domain interface.
Article
Chemistry, Physical
Yangyang Zhang, Donghui Liu, Yiyang Zhang, Yachong Guo, Wenfei Li, Fabrice Thalmann
Summary: This article describes a coarse-grained model of POPC and DOPC lipid peroxides and discusses their predicted structure and the influence of hydration. In addition, electron and neutron scattering length density profiles of the simulated bilayers are provided.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Polymer Science
Kuan-Hsuan Shen, Mengdi Fan, Lisa M. Hall
Summary: Molecular dynamics simulations with generic bead-spring models have been used to study the molecular-scale behavior and structure-property relationships of various polymeric systems. While this coarse-grained modeling approach provides computational efficiency and flexibility in considering different chemistries, additional complexity may be needed to appropriately describe phenomena in ion-containing polymeric systems.
Article
Polymer Science
Juan J. de Pablo, Heyi Liang, Michael A. Webb, Manasi Chawathe, Denis Bendejacq
Summary: Understanding and predicting the behavior of galactomannans in aqueous solutions is important for various applications. In this study, a coarse-grained model of guar gum, a type of galactomannan, was developed and validated. The model showed good agreement with experimental results in terms of chain structure, aggregate formation, and solution viscosity. The behavior of guar gum in water was explained using scaling theory for polymers in good solvents.
Article
Chemistry, Physical
Christopher C. Walker, Garrett A. Meek, Theodore L. Fobe, Michael R. Shirts
Summary: In this paper, a Python-based simulation framework, cg_openmm, is introduced for modeling coarse-grained hetero-oligomers and screening them for structural and thermodynamic characteristics. The framework includes tools for building topology, setting up simulations, and analyzing thermodynamic and structural properties. The capabilities of cg_openmm are demonstrated on a simple coarse-grained model, showing the formation of stable helices through cooperative folding transitions and the tunability of helix geometries and stabilities by manipulating force-field parameters.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2021)
Article
Chemistry, Physical
Diego Ugarte La Torre, Shoji Takada
Summary: A lipid-protein interaction model was developed for coarse-grained molecular dynamics simulations, showing good agreement with experimental results and prior knowledge. This model has been implemented in the publicly available software, CafeMol.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Fabian Grunewald, Mats H. Punt, Elizabeth E. Jefferys, Petteri A. Vainikka, Melanie Koenig, Valtteri Virtanen, Travis A. Meyer, Weria Pezeshkian, Adam J. Gormley, Maarit Karonen, Mark S. P. Sansom, Paulo C. T. Souza, Siewert J. Marrink
Summary: The study develops a consistent strategy to accurately parametrize carbohydrate molecules within the framework of Martini 3 model and demonstrates the validity and transferability of this approach through various test cases.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Multidisciplinary
Ilias Patmanidis, Paulo C. T. Souza, Selim Sami, Remco W. A. Havenith, Alex H. de Vries, Siewert J. Marrink
Summary: Self-assembly is a widely observed process, but understanding its dynamic pathways and molecular details of the final structures is challenging. This study addresses this problem by using coarse-grained modeling and successfully optimizing parameters for a cyanine dye. Simulations provide information on the time-dependent local arrangement of the dye during self-assembly, and guidelines for designing and optimizing similar self-assembling nanomaterials.
NANOSCALE ADVANCES
(2022)
Article
Chemistry, Physical
Stephan Thaler, Maximilian Stupp, Julija Zavadlav
Summary: Neural network potentials are a natural choice for coarse-grained models, but they suffer from finite data effects when trained bottom-up via force matching. In this work, the authors demonstrate that relative entropy training is more data efficient and improves free energy surfaces and sensitivity to prior potentials. The findings support the use of training objectives beyond force matching for improving the accuracy and reliability of coarse-grained neural network potentials.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
Xukai Jiang, Yuliang Sun, Kai Yang, Bing Yuan, Tony Velkov, Lushan Wang, Jian Li
Summary: The study developed an asymmetric outer membrane (OM) model and used molecular dynamics simulations to investigate the interaction dynamics of lipopolysaccharide (LPS)-containing OM with the polymyxins. It was discovered that polymyxin molecules penetrated the OM core sugar region but were trapped before entering the lipid A region due to a major free energy barrier at the LPS inner core and lipid A interface. Calcium ions were found to inhibit the penetration of polymyxins into the hydrophobic region of the OM by mediating cross-linking interactions between LPS molecules.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Chemistry, Multidisciplinary
Param Punj Singh, Raghavan Ranganathan
Summary: Organisms have an evolutionary advantage in forming complex structures with superior mechanical properties, and efforts to mimic these structures for synthesizing high-performance materials have seen rapid growth thanks to advances in microscopy and testing methodologies. In this study, the mechanical and viscoelastic behavior of nacre-like microstructures was investigated using molecular dynamics simulations. It was found that the microstructure and polymer-crystal interactions play a significant role in the mechanical properties and viscoelastic behavior of the material.
Article
Chemistry, Applied
Jiu Pang, Aleksandar Y. Mehandzhiyski, Igor Zozoulenko
Summary: In this study, we used Martini 3 molecular dynamics simulations to investigate the regeneration of cellulose at a scale comparable to experiments. The structural changes and formation of cellulose sheets and crystallites were monitored using X-ray diffraction (XRD) curves. Our results show that the calculated coarse-grained morphologies of regenerated cellulose are transformed to cellulose II, which is in good agreement with experimental observations.
CARBOHYDRATE POLYMERS
(2023)
Article
Chemistry, Physical
Ainara Claveras Cabezudo, Christina Athanasiou, Alexandros Tsengenes, Rebecca C. Wade
Summary: Reducing the nonbonded interactions between protein and water enables protein encapsulation in phospholipid micelles and bilayers.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Multidisciplinary
Xiaobing Li, Pierre-Andre Cazade, Pan Qi, Damien Thompson, Cunlan Guo
Summary: This study investigates the modulation of charge transport in peptide self-assembled monolayers by adjusting the position of charged residues and creating different protonation patterns. The results show that the modulation of hydrogen bonding and electrostatic interactions through pH changes affects charge transport in the peptide SAMs.
CHINESE CHEMICAL LETTERS
(2023)
Article
Pharmacology & Pharmacy
Oisin N. Kavanagh, Shayon Bhattacharya, Luke Marchetti, Robert Elmes, Finbarr O'Sullivan, John P. Farragher, Shane Robinson, Damien Thompson, Gavin M. Walker
Summary: Drug-mediated correction of abnormal biological zinc homeostasis is important for treating neurodegeneration, cancer, and viral infections. Our study provides evidence that hydroxychloroquine, a potential treatment for COVID-19, does not bind and transport zinc through ionophoric mechanisms as previously claimed.
Article
Chemistry, Multidisciplinary
Santi P. Rath, Damien Thompson, Sreebrata Goswami, Sreetosh Goswami
Summary: The study presents the design of temperature-resilient molecular memristors that allow for control of electronic transport by manipulating the interactions between molecules and counterions. These memristors exhibit various functionalities within a single device, and offer a deterministic design route for engineering neuromorphic devices.
ADVANCED MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Syed Abdul Ahad, Shayon Bhattacharya, Seamus Kilian, Michela Ottaviani, Kevin M. M. Ryan, Tadhg Kennedy, Damien Thompson, Hugh Geaney
Summary: Researchers have created a 3D framework of a carbon paper substrate decorated with lithiophilic nanowires to address the issues of uncontrolled dendrite formation and build-up of dead Li in Lithium (Li) metal batteries. The study shows that this design can effectively prevent dendrite formation and achieve stable cycling performance.
Article
Nanoscience & Nanotechnology
Christian A. Nijhuis, Ziyu Zhang, Francis Adoah, Cameron Nickle, Senthil Kumar Karuppannan, Lejia Wang, Li Jiang, Anton Tadich, Bruce Cowie, Teddy Salim, Dong-Chen Qi, Damien Thompson, Enrique Del Barco
Summary: This paper investigates the mechanism of charge transport across molecular wires and finds that it can be switched between the normal and Marcus Inverted regions by tuning the molecule-electrode coupling strength and the tunneling distance. The results also suggest that weak molecule-electrode coupling is important for pushing the junctions into the Marcus Inverted Region.
ADVANCED ELECTRONIC MATERIALS
(2023)
Article
Chemistry, Physical
Reabetswe R. Zwane, Joaquin Klug, Sarah Guerin, Damien Thompson, Anthony M. Reilly
Summary: In recent years, computational methods, particularly dispersion-corrected density functional theory (DFT), have been used to predict and design the mechanical response of molecular crystals. The results show that the supramolecular packing, such as extended H-bond or ir-ir networks, plays a crucial role in determining the mechanical behavior of the crystals. This has important implications for drug development.
JOURNAL OF PHYSICAL CHEMISTRY C
(2023)
Article
Nanoscience & Nanotechnology
Talia Bergaglio, Shayon Bhattacharya, Damien Thompson, Peter Niraj Nirmalraj
Summary: Understanding the effect of over-the-counter drugs on red blood cells is important for medical research. This study used digital holotomography to monitor the changes in red blood cells caused by ibuprofen in real-time and found that high concentrations of ibuprofen disrupt the structure and order of the red blood cell membrane.
ACS NANOSCIENCE AU
(2023)
Article
Nanoscience & Nanotechnology
Peter Niraj Nirmalraj, Marta D. Rossell, Walid Dachraoui, Damien Thompson, Michael Mayer
Summary: This study demonstrates the use of liquid-based atomic force microscope and graphene liquid-cell-based scanning transmission electron microscope to observe chemically induced protein unfolding. The results show that fully folded ferritin proteins transform into rings after urea treatment but not after guanidinium treatment. Nanorings are a specific signature of denaturation of holo-ferritins after exposure to sufficiently high urea concentrations. The study also suggests that electrostatic destabilization triggers denaturation of ferritin as urea makes direct contact with the protein and disrupts the water H-bonding network in the ferritin solvation shell.
ACS APPLIED MATERIALS & INTERFACES
(2023)
Article
Chemistry, Medicinal
Shubham Vishnoi, Shayon Bhattacharya, Erica M. Walsh, Grace Ilevbare Okoh, Damien Thompson
Summary: Peptides are sustainable alternatives for GPCR-linked disorders. Dual agonist peptides targeting GCGR and GLP-1R can address both diabetes and obesity, offering improved glycemic and weight loss control. In this study, optimized peptide sequences with predicted molecular binding profiles for dual agonism are designed and modeled, showing potential for future experimental testing.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2023)
Article
Chemistry, Multidisciplinary
Yuehui Wang, Shuaijie Liu, Lingling Li, Hui Li, Yuanyuan Yin, Sigal Rencus-Lazar, Sarah Guerin, Wengen Ouyang, Damien Thompson, Rusen Yang, Kaiyong Cai, Ehud Gazit, Wei Ji
Summary: This study systematically explored the supramolecular engineering of amino acid-based assemblies and found that chemical modification of acetylated amino acids can enhance their piezoelectric response. By fabricating an L-AcW crystal-based piezoelectric power nanogenerator, the illumination of a light-emitting diode (LED) was successfully demonstrated using the power output of an amino acid-based piezoelectric nanogenerator.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Correction
Nanoscience & Nanotechnology
Sreetosh Goswami, Santi P. Rath, Damien Thompson, Svante Hedstrom, Meenakshi Annamalai, Rajib Pramanick, B. Robert Ilic, Soumya Sarkar, Sonu Hooda, Christian A. Nijhuis, Jens Martin, R. Stanley Williams, Sreebrata Goswami, T. Venkatesan
NATURE NANOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
Zhenyu Yang, Pierre-Andre Cazade, Jin-Liang Lin, Zhou Cao, Ningyue Chen, Dongdong Zhang, Lian Duan, Christian A. Nijhuis, Damien Thompson, Yuan Li
Summary: The research team has achieved fully reversible in-situ mechano-optoelectronic switching by bending the supporting electrodes to maximize aggregation-induced emission. Their study demonstrates the potential for new applications in soft electronics by optimizing the interplay between mechanical force and optics.
NATURE COMMUNICATIONS
(2023)
Article
Materials Science, Multidisciplinary
Thangavel Vijayakanth, Bin Xue, Sarah Guerin, Sigal Rencus-Lazar, Natalia Fridman, Damien Thompson, Yi Cao, Ehud Gazit
Summary: Supramolecular helical structures formed by the assembly of biological and bio-inspired building blocks have potential applications in sustainable biomedical technologies and electronics. The present study introduces a strategy to precisely formulate these structures using N-terminal protected aromatic pyridyl amino acids, which display helicity at the molecular level. The helical structure is stabilized by intermolecular hydrogen bonding. The study also demonstrates the influence of amino acid chirality on supramolecular crystal packing, self-assembly, and electromechanical properties.
JOURNAL OF MATERIALS CHEMISTRY C
(2023)
Article
Nanoscience & Nanotechnology
Oguzhan Maraba, Shayon Bhattacharya, Martin Conda-Sheridan, Damien Thompson
Summary: Peptide self-assemblies serve as a natural template for designing bio-inspired functional materials. In this study, the researchers investigate the physical driving forces for self-assembly at the molecular level using a complex peptide called microtubule-binding domain (MBD) of tau protein. Through extensive molecular dynamics simulations, they analyze the effects of mutations on the stability and morphology of the peptide assemblies. The findings suggest that the mutations destabilize the supramolecular packing and may explain the mutation-induced toxicity levels observed in neurodegenerative diseases.
Article
Nanoscience & Nanotechnology
Santu Bera, Pierre-Andre Cazade, Shayon Bhattacharya, Sarah Guerin, Moumita Ghosh, Francesca Netti, Damien Thompson, Lihi Adler-Abramovich
Summary: This study reports the design of rigid hybrid hydrogels produced by sequence engineering of a new series of ultra-short collagen-mimicking tripeptides, demonstrating the importance of sequence engineering to design functional peptide motifs with desired physicochemical and electromechanical properties and revealing co-assembly as a promising strategy for the utilization of small, readily accessible biomimetic building blocks to generate hybrid biomolecular assemblies with structural heterogeneity and functionality of natural materials.
ACS APPLIED MATERIALS & INTERFACES
(2022)