Article
Engineering, Multidisciplinary
Chenwen Tian, Shuaiqi Fan, Juan Du, Zhikun Zhou, Ziguang Chen, Florin Bobaru
Summary: This paper presents a bond-based peridynamic (PD) advection-reaction-diffusion model for simulating processes involving chemical reactions, flows, and diffusion. The model considers both linear and nonlinear dependencies, and solves a system of coupled PD equations for each substance numerically. The model is verified and validated through comparisons with classical models and experiments in 1D and 2D, and is also applied to simulate advection-reaction-diffusion in heterogeneous media and polymer degradation through hydrolysis and diffusion.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Michelle Redhair, William M. Atkins
Summary: The article discusses the importance of ligand-dependent changes in protein conformation in biology, introducing the induced fit and conformational selection mechanisms, and explaining their impact on protein substrate specificity, promiscuity, and regulatory properties. It also presents a new perspective based on interactions between protein ensembles and ligand ensembles, and describes how probing protein ensembles with multiple ligands can optimize mechanistic information.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2021)
Article
Mathematics, Applied
S. C. Generalis, A. De Wit, P. M. J. Trevelyan
Summary: This study investigates the properties of bimolecular reaction-diffusion fronts when reactants A and B are dissolved in two immiscible solvents. The study reveals that in immiscible systems, the direction of bimolecular reaction-diffusion fronts can change up to four times, while in miscible systems, only two changes of direction are possible. Additionally, the study identifies the conditions under which two local maxima in the reaction rate can exist.
APPLIED MATHEMATICS LETTERS
(2023)
Article
Chemistry, Physical
Pakorn Pasitsuparoad, Gonzalo Angulo
Summary: This study investigates the effects of liquid crystal structure on chemical reactions, focusing on anisotropy using fluorescence quenching to study photo-induced intermolecular electron transfer. By conducting steady state and time resolved measurements in isotropic media at different temperatures and viscosities, electron transfer parameters independent of the solvent are extracted. Developing diffusion-reaction models with different levels of anisotropy allows for physically meaningful values to be obtained for all parameters entering reactivity, showing how to adapt models to complex environments.
JOURNAL OF MOLECULAR LIQUIDS
(2021)
Article
Chemistry, Physical
Naresh C. Osti, Bishnu Prasad Thapaliya, Ray A. Matsumoto, Arjun Bansal, Xiaobo Lin, Peter T. Cummings, Madhusudan Tyagi, Sheng Dai, Eugene Mamontov
Summary: This study reveals that LiTFSI has a significant impact on the diffusivity of organic solvents in supercapacitors, with a reduction of approximately 50% in solvent diffusivity when the concentration is below 1 M. These findings provide important guidance for formulating electrolytes to enhance the performance of energy storage devices.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Aisha Ahsan, Luiza Buimaga-Iarinca, Thomas Nijs, Sylwia Nowakowska, Sk Rejaul, S. Fatemeh Mousavi, Mehdi Heydari, Meike Stoehr, Sameena S. Zaman, Cristian Morari, Lutz H. Gade, Thomas A. Jung
Summary: Host-guest architectures provide ideal systems for investigating site-specific physical and chemical effects. In this study, we found that the symmetry, registry, lateral packing, and adsorption height of small clusters formed upon condensation are modified by the presence of cycloalkanes in confined spaces. While cyclopentane and cycloheptane show cooperativity upon filling, cyclooctane and to a lesser degree cyclohexane redistribute to more favorable adsorption sites. This site-specific modification of interaction and behavior is crucial for applications of porous materials in gas storage or catalysis.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemistry & Molecular Biology
Marco van den Noort, Marijn de Boer, Bert Poolman
Summary: This study demonstrates that different ligands induce distinct bound conformations, and by changing the free energies of available conformations, ligand affinity can be adjusted. Experimental data on the maltose-binding protein (MBP) from Escherichia coli reveals that ligand affinity can be modulated through altering conformations.
JOURNAL OF MOLECULAR BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Alessandro Nicola Nardi, Alessio Olivieri, Andrea Amadei, Riccardo Salvio, Marco D'Abramo
Summary: In this study, the kinetics of hydroxide-promoted hydrolysis of phosphoric diesters were modeled using a hybrid quantum/classical approach. The results suggest that the hydrolysis occurs through a concerted A(N)D(N) mechanism, with no formation of penta-coordinated intermediates. This modeling method has the potential to predict rate constants and reactivities/selectivities in complex environments.
Article
Polymer Science
Ramon Novoa-Carballal, Manuel Martin-Pastor, Eduardo Fernandez-Megia
Summary: The IF-STD method is proposed for detecting hidden nuclei in polymer H-1 NMR spectra in solution NMR. By saturating the IF region, the presence of hidden nuclei is confirmed through a difference spectrum.
Article
Engineering, Marine
Jan Majcher, Rory Quinn, Thomas Smyth, Ruth Plets, Chris McGonigle, Kieran Westley, Fabio Sacchetti, Mark Coughlan
Summary: The large number of historic metal-hulled shipwrecks on the seabed has significant implications for the marine environment, heritage management, and spatial planning. This study combines high-resolution data and computational fluid dynamics to investigate the interplay between hydro- and sediment-dynamics and the deterioration of submerged tidally-influenced shipwrecks. The findings reveal complex patterns of wake and horseshoe vortices, as well as the correlation between wall shear stress and damage on the wrecks, providing insights for site management and offshore engineering.
Article
Biochemical Research Methods
Sara Ibrahim Omar, Meng Zhao, Rohith Vedhthaanth Sekar, Sahar Arbabi Moghadam, Jack A. Tuszynski, Michael T. Woodside
Summary: The coronavirus responsible for COVID-19 controls viral protein production through a unique RNA pseudoknot structure, which may be a potential target for treating the disease. Computational modeling revealed multiple possible conformations of the SARS-CoV-2 pseudoknot, providing insight for future experiments and drug discovery efforts. The study also identified unusual structures involving RNA threading through helical junctions, which could aid in understanding and developing treatments for SARS-CoV-2.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Kiyoshi Fujisawa, Taisei Kataoka, Kohei Terashima, Haruka Kurihara, Felipe de Santis Goncalves, Nicolai Lehnert
Summary: Due to its important roles in biology, nitrogen monoxide (NO) is widely studied and considered as one of the most fascinating molecules in chemistry. NO acts as a redox active ligand to transition metal ions, forming metal-NO (M-NO) complexes. The electronic structure of the M-NO unit requires extensive spectroscopic and theoretical studies. In this study, the dioxygen reactivity of two Ni-NO complexes with different ligands (hindered N3 and less hindered N2) was investigated and characterized.
Article
Chemistry, Physical
Aishani Ghosal
Summary: This paper explores a macromolecule with two competitive binding sites and calculates various parameters under different levels of ligand competition, finding that increased competition decreases the values of related additive functionals.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Huiyan Liu, Zhi Liu, Chaodan Pu
Summary: This article investigates the growth process of CdS colloidal quantum dots and finds that the size broadening is caused by different growth rates of CdS colloidal quantum dots with different morphologies. The study also reveals that the addition of chloride ions can more effectively reduce the size distribution of CdS colloidal quantum dots.
Article
Chemistry, Physical
David Robert Daniels
Summary: This study provides an expression for the diffusion-limited reaction rate on a curved surface or membrane and applies it to calculating the receptor-ligand association rate. The research finds that the receptor-ligand reaction rates can be significantly reduced due to the effect of locally induced membrane curvature or geometry.
CHEMICAL PHYSICS LETTERS
(2022)
Article
Chemistry, Physical
Huan-Xiang Zhou
Summary: Biomolecular condensates exhibit viscoelastic properties that can be captured by a simple model, with modulation of intermolecular interactions affecting the components differently. The tendency of condensates to fuse is influenced by interfacial tension and viscosity, with shear relaxation dynamics playing a role in fusion speed. These insights contribute to bridging the gap between the biology and physics of biomolecular condensates.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Yuqin Yang, Hao Dong, Huan-Xiang Zhou
Summary: The study found that cholesterol has a significant impact on the distribution of the anti-influenza drug amantadine in bilayers, with cholesterol reducing the amount of amantadine in the membrane mainly by perturbing the bilayer structure and dynamics. Surrounding lipids stabilize amantadine by wrapping their tails around the drug molecule, a function compromised in the presence of cholesterol due to increased lipid tail order.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Physical
Xu Dong, Ling-Yun Qin, Zhou Gong, Sanbo Qin, Huan-Xiang Zhou, Chun Tang
Summary: Nonspecific binding of crowder proteins with functional proteins is common in vivo, with bovine serum albumin weakly but preferentially interacting with the histidine carrier protein (HPr). This competition with HPr's specific partner protein, EIN, decreases the binding affinity and accelerates dissociation of the native complex, while Ficoll-70 stabilizes the complex and slows dissociation. Atomistic modeling of macromolecular crowding rationalizes the experimental data and provides insights into protein-crowder interactions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Chemistry, Physical
Konstantinos Mazarakos, Huan-Xiang Zhou
Summary: In this study, a mean-field theoretical model and molecular dynamics simulations are used to demonstrate that the multiphase organization of multi-component condensates undergoes a second phase transition, driven by the difference in attraction strengths between different components. The phase transitions are observed by decreasing the temperature, leading to condensate separation from the bulk phase and component demixing within the condensates. Molecular dynamics simulations of model mixtures verify the existence of a critical temperature for demixing and predicted binodals.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Divya Kota, Huan-Xiang Zhou
Summary: This study found that macromolecular regulators have effects on the material properties of biomolecular condensates, including phase equilibrium, interfacial tension, viscoelasticity, fusion speed, etc. These results illustrate the opportunities for tuning material properties.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biology
Aayush Gupta, Souvik Dey, Alan Hicks, Huan-Xiang Zhou
Summary: This study developed generative autoencoders that can learn from short molecular dynamics simulations and generate full conformational ensembles of intrinsically disordered proteins.
COMMUNICATIONS BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Sanbo Qin, Alan Hicks, Souvik Dey, Ramesh Prasad, Huan-Xiang Zhou
Summary: This study identified the membrane-association characteristics of intrinsically disordered regions (IDRs) in proteins and developed a web server called ReSMAP for predicting residue-specific membrane-association propensities from IDR sequences.
Article
Chemistry, Physical
Souvik Dey, Matthew MacAinsh, Huan-Xiang Zhou
Summary: For intrinsically disordered proteins (IDPs), the dynamics of the backbone play a key role in encoding their function. The dynamics are regulated by local interactions, secondary structures, and glycines. These sequence-dependent changes in backbone dynamics allow IDPs to respond to binding partners in a versatile manner.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Konstantinos Mazarakos, Ramesh Prasad, Huan-Xiang Zhou
Summary: Phase separation of intrinsically disordered proteins (IDPs) is a phenomenon associated with many essential cellular processes. However, there is still a difficulty in computing the binodal from molecular dynamics simulations of IDPs. In this study, a new method called SpiDec is proposed, which allows for the accurate determination of the phase equilibrium of IDPs.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Matthew MacAinsh, Huan-Xiang Zhou
Summary: Tau, an intrinsically disordered protein, binds to both microtubules and acidic membranes. This study used molecular dynamics simulations to investigate the dynamic binding of Tau to an acidic membrane. The simulations validated the interaction between amphipathic helices in Tau and the membrane, and showed similarities and differences in residue contacts between Tau and microtubules. This mimicry facilitates both the anchoring of microtubules to membranes and the transfer of Tau from membranes to microtubules.
Article
Chemistry, Physical
Huan-Xiang Zhou
Summary: This article introduces an approach for estimating the lower and upper bounds of sample data using O(N) operations. The approach calculates the mean values of the smallest and largest x values in N-point samples and fits them as functions of N to obtain the estimates for the bounds. Application to synthetic data demonstrates the accuracy and reliability of this approach.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Souvik Dey, Huan-Xiang Zhou
Summary: This study used molecular dynamics simulations to investigate the regulation of the IDP N-WASP, finding that intramolecular interactions keep N-WASP in an autoinhibited state and PIP2 binding can activate it by freeing the acidic motif, which interacts with Arp2/3 to initiate actin polymerization. Competition exists between PIP2 and the acidic motif for binding to the basic region. Even at a 30% PIP2 level in the membrane, the acidic motif only contacts the basic region in 8.5% of the population.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Multidisciplinary Sciences
Johansen B. Amin, Miaomiao He, Ramesh Prasad, Xiaoling Leng, Huan-Xiang Zhou, Lonnie P. Wollmuth
Summary: NMDA receptors have two gates that are regulated by distinct subunits, with one gate mainly regulating single channel events and the other gate mainly regulating entry and exit from clusters. The unique kinetics of NMDARs contribute to their role in synaptic signaling, with clusters of rapid opening and closing separated by long silent periods.
NATURE COMMUNICATIONS
(2023)
Article
Biology
Sean T. Smrt, Cristian A. Escobar, Souvik Dey, Timothy A. Cross, Huan-Xiang Zhou
Summary: Mtb infects a quarter of the worldwide population and the rising drug resistance makes it urgent to better understand Mtb cell division. The study reveals that the transmembrane protein FtsQ may serve as a membrane anchor of the Mtb Z-ring, and its disordered cytoplasmic region interacts with multiple partners, indicating its potential role in cell division and as a drug target.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biology
Guodong Hu, Huan-Xiang Zhou
Summary: The SAM/SAH riboswitch binds SAM and SAH with similar affinities. Molecular dynamics simulations reveal the role of Mg2+ ions in stabilizing the RNA structure, widening the groove for ligand entry, and facilitating ribosome binding. Mg2+ plays vital roles in the function of the SAM/SAH riboswitch.
COMMUNICATIONS BIOLOGY
(2023)