keyword
https://read.qxmd.com/read/38537131/analyzing-lipid-membrane-defects-via-a-coarse-grained-to-triangulated-surface-map-the-role-of-lipid-order-and-local-curvature-in-molecular-binding
#1
JOURNAL ARTICLE
Rianne W I van der Pol, Bregje W Brinkmann, G J Agur Sevink
Lipid packing defects are known to serve as quantitative indicators for protein binding to lipid membranes. This paper presents a protocol for mapping molecular lipid detail onto a triangulated continuum leaflet representation. Besides establishing the desired forward counterpart to the existing inverse TS2CG map, this coarse-grained to triangulated surface (CG2TS) map enables straightforward extraction of the defect characteristics for any membrane geometry found in nature. We have applied our protocol to investigate the role of local curvature and varying lipid packing on the defect constant π...
March 27, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38532625/two-component-macrophage-model-for-active-phagocytosis-with-pseudopod-formation
#2
JOURNAL ARTICLE
Shuo Wang, Shuhao Ma, He Li, Ming Dao, Xuejin Li, George Em Karniadakis
Macrophage phagocytosis is critical for the immune response, homeostasis regulation and tissue repair. This intricate process involves complex changes in cell morphology, cytoskeletal reorganization, and various receptor-ligand interactions controlled by mechanical constraints. However, there is a lack of comprehensive theoretical and computational models that investigate the mechanical process of phagocytosis in the context of cytoskeletal rearrangement. To address this issue, we propose a novel coarse-grained mesoscopic model that integrates a fluid-like cell membrane and a cytoskeletal network to study the dynamic phagocytosis process...
March 25, 2024: Biophysical Journal
https://read.qxmd.com/read/38532339/hippo-histogram-based-pseudo-potential-for-scoring-protein-ssrna-fragment-based-docking-poses
#3
JOURNAL ARTICLE
Anna Kravchenko, Sjoerd Jacob de Vries, Malika Smaïl-Tabbone, Isaure Chauvot de Beauchene
BACKGROUND: The RNA-Recognition motif (RRM) is a protein domain that binds single-stranded RNA (ssRNA) and is present in as much as 2% of the human genome. Despite this important role in biology, RRM-ssRNA interactions are very challenging to study on the structural level because of the remarkable flexibility of ssRNA. In the absence of atomic-level experimental data, the only method able to predict the 3D structure of protein-ssRNA complexes with any degree of accuracy is ssRNA'TTRACT, an ssRNA fragment-based docking approach using ATTRACT...
March 26, 2024: BMC Bioinformatics
https://read.qxmd.com/read/38531147/mob-cbam-a-dual-channel-attention-based-deep-learning-generalizable-model-for-breast-cancer-molecular-subtypes-prediction-using-mammograms
#4
JOURNAL ARTICLE
Iqra Nissar, Shahzad Alam, Sarfaraz Masood, Mohammad Kashif
BACKGROUND AND OBJECTIVE: Deep Learning models have emerged as a significant tool in generating efficient solutions for complex problems including cancer detection, as they can analyze large amounts of data with high efficiency and performance. Recent medical studies highlight the significance of molecular subtype detection in breast cancer, aiding the development of personalized treatment plans as different subtypes of cancer respond better to different therapies. METHODS: In this work, we propose a novel lightweight dual-channel attention-based deep learning model MOB-CBAM that utilizes the backbone of MobileNet-V3 architecture with a Convolutional Block Attention Module to make highly accurate and precise predictions about breast cancer...
March 10, 2024: Computer Methods and Programs in Biomedicine
https://read.qxmd.com/read/38530715/instrument-tissue-interaction-detection-framework-for-surgical-video-understanding
#5
JOURNAL ARTICLE
Wenjun Lin, Yan Hu, Huazhu Fu, Mingming Yang, Chin-Boon Chng, Ryo Kawasaki, Cheekong Chui, Jiang Liu
Instrument-tissue interaction detection task, which helps understand surgical activities, is vital for constructing computer-assisted surgery systems but with many challenges. Firstly, most models represent instrument-tissue interaction in a coarse-grained way which only focuses on classification and lacks the ability to automatically detect instruments and tissues. Secondly, existing works do not fully consider relations between intra-and inter-frame of instruments and tissues. In the paper, we propose to represent instrument-tissue interaction as ⟨instrument class, instrument bounding box, tissue class, tissue bounding box, action class⟩ quintuple and present an Instrument-Tissue Interaction Detection Network (ITIDNet) to detect the quintuple for surgery videos understanding...
March 26, 2024: IEEE Transactions on Medical Imaging
https://read.qxmd.com/read/38528959/formation-of-low-pressure-reaction-textures-during-near-isothermal-exhumation-of-hot-orogenic-crust-bohemian-massif-austria
#6
JOURNAL ARTICLE
Dominik Sorger, Christoph A Hauzenberger, Fritz Finger, Manfred Linner, Etienne Skrzypek, Simon Schorn
Two types of aluminous paragneiss from the Loosdorf complex (Bohemian Massif, NE Austria) contain coarse-grained granulite assemblages and retrograde reaction textures that are investigated to constrain the post-peak history of the Gföhl unit in the southern Bohemian Massif. Both types have a peak assemblage garnet-biotite-sillimanite-plagioclase-K-feldspar-quartz-granitic melt ± kyanite ± ilmenite ± rutile, recording peak metamorphic conditions of <mml:math xmlns:mml="https://www...
January 2024: J Metamorph Geol
https://read.qxmd.com/read/38528664/hysteresis-elimination-for-an-anisotropic-liquid-crystal-model-via-molecule-design-and-replica-exchange-optimization
#7
JOURNAL ARTICLE
Akie Kowaguchi, Paul E Brumby, Kenji Yasuoka
The phenomenon of hysteresis in simulations, in which a system's current state is correlated to previous states and inhibits the transition to a more stable phase, may often lead to misleading results in physical chemistry. In this study, in addition to the replica exchange method (REM), a novel approach was taken by combining an evolution strategy based on the evolutionary principles of nature to predict phase transitions for the Hess-Su liquid-crystal model. In this model, an anisotropy term is added to the simple 6-12 Lennard-Jones model to intuitively reproduce the behavior of liquid crystals...
March 25, 2024: Journal of Chemical Information and Modeling
https://read.qxmd.com/read/38526088/priorities-opportunities-and-challenges-for-integrating-microorganisms-into-earth-system-models-for-climate-change-prediction
#8
JOURNAL ARTICLE
J T Lennon, R Z Abramoff, S D Allison, R M Burckhardt, K M DeAngelis, J P Dunne, S D Frey, P Friedlingstein, C V Hawkes, B A Hungate, S Khurana, S N Kivlin, N M Levine, S Manzoni, A C Martiny, J B H Martiny, N K Nguyen, M Rawat, D Talmy, K Todd-Brown, M Vogt, W R Wieder, E J Zakem
Climate change jeopardizes human health, global biodiversity, and sustainability of the biosphere. To make reliable predictions about climate change, scientists use Earth system models (ESMs) that integrate physical, chemical, and biological processes occurring on land, the oceans, and the atmosphere. Although critical for catalyzing coupled biogeochemical processes, microorganisms have traditionally been left out of ESMs. Here, we generate a "top 10" list of priorities, opportunities, and challenges for the explicit integration of microorganisms into ESMs...
March 25, 2024: MBio
https://read.qxmd.com/read/38525030/range-expansion-can-promote-the-evolution-of-plastic-generalism-in-coarse-grained-landscapes
#9
JOURNAL ARTICLE
Caitlin M Miller, Jeremy A Draghi
Phenotypic plasticity is one way for organisms to deal with variable environments through generalism. However, plasticity is not found universally and its evolution may be constrained by costs and other limitations such as complexity: the need for multiple mutational steps before the adaptation is realized. Theory predicts that greater experienced heterogeneity, such as organisms may encounter when spatial heterogeneity is fine-grained relative to dispersal, should favor the evolution of a broader niche. Here we tested this prediction via simulation...
April 2024: Evolution Letters
https://read.qxmd.com/read/38520347/minimal-coarse-grained-models-of-polar-solvent-for-electrolytes-stockmayer-versus-dumbbell
#10
JOURNAL ARTICLE
Xinqiang Liu, Xian Kong
This study explores the potential of the dumbbell solvent as a minimal model for understanding electrolyte solutions in polar solvents. Our investigation involves a comparative analysis of the dumbbell model and the Stockmayer model, focusing on ion solvation and ion-ion correlations. We examine electrolytes containing symmetric monovalent salts dissolved in polar solvents while varying the ion density and solvent polarity. Both models predict an augmented solvent coordination number around ions as the solvent polarity increases, with the dumbbell solvent displaying a more pronounced effect...
March 23, 2024: Journal of Physical Chemistry. B
https://read.qxmd.com/read/38518302/systematic-coarse-graining-of-environments-for-the-nonperturbative-simulation-of-open-quantum-systems
#11
JOURNAL ARTICLE
Nicola Lorenzoni, Namgee Cho, James Lim, Dario Tamascelli, Susana F Huelga, Martin B Plenio
Conducting precise electronic-vibrational dynamics simulations of molecular systems poses significant challenges when dealing with realistic environments composed of numerous vibrational modes. Here, we introduce a technique for the construction of effective phonon spectral densities that capture accurately open-system dynamics over a finite time interval of interest. When combined with existing nonperturbative simulation tools, our approach can reduce significantly the computational costs associated with many-body open-system dynamics...
March 8, 2024: Physical Review Letters
https://read.qxmd.com/read/38516954/valency-of-ligand-receptor-binding-from-pair-potentials
#12
JOURNAL ARTICLE
William Morton, Robert Vácha, Stefano Angioletti-Uberti
Coarse grained molecular dynamics simulations have been crucial for investigating the dynamics of nanoparticle uptake by cell membranes via ligand-receptor interactions. These models have enabled researchers to evaluate the effects of nanoparticle size, shape, and ligand distribution on cellular uptake. However, when pair potentials are used to represent ligand-receptor interactions, the number of receptors interacting with one ligand, valency, may vary. We demonstrate that the curvature of a nanoparticle, strength of ligand-receptor interactions, and ligand or receptor concentration change the valency, ranging from 3...
March 22, 2024: Journal of Chemical Theory and Computation
https://read.qxmd.com/read/38514440/colabind-a-cloud-based-approach-for-prediction-of-binding-sites-using-coarse-grained-simulations-with-molecular-probes
#13
JOURNAL ARTICLE
Georgy Andreev, Max Kovalenko, Marine E Bozdaganyan, Philipp S Orekhov
Binding site prediction is a crucial step in understanding protein-ligand and protein-protein interactions (PPIs) with broad implications in drug discovery and bioinformatics. This study introduces Colabind, a robust, versatile, and user-friendly cloud-based approach that employs coarse-grained molecular dynamics simulations in the presence of molecular probes, mimicking fragments of drug-like compounds. Our method has demonstrated high effectiveness when validated across a diverse range of biological targets spanning various protein classes, successfully identifying orthosteric binding sites, as well as known druggable allosteric or PPI sites, in both experimentally determined and AI-predicted protein structures, consistently placing them among the top-ranked sites...
March 21, 2024: Journal of Physical Chemistry. B
https://read.qxmd.com/read/38512104/understanding-and-fine-tuning-the-propensity-of-atp-driven-liquid-liquid-phase-separation-with-oligolysine
#14
JOURNAL ARTICLE
Qiang Zhu, Yongxian Wu, Ray Luo
Liquid-liquid phase separation (LLPS) plays a pivotal role in the organization and functionality of living cells. It is imperative to understand the underlying driving forces behind LLPS and to control its occurrence. In this study, we employed coarse-grained (CG) simulations as a research tool to investigate systems comprising oligolysine and adenosine triphosphate (ATP) under conditions of various ionic concentrations and oligolysine lengths. Consistent with experimental observations, our CG simulations captured the formation of LLPS upon the addition of ATP and tendency of dissociating under high ionic concentration...
March 21, 2024: Physical Chemistry Chemical Physics: PCCP
https://read.qxmd.com/read/38511659/single-molecule-analysis-of-solvent-responsive-mechanically-interlocked-ring-polymers-and-the-effects-of-nanoconfinement-from-coarse-grained-simulations
#15
JOURNAL ARTICLE
Diego Becerra, Alexander R Klotz, Lisa M Hall
In this study, we simulate mechanically interlocked semiflexible ring polymers inspired by the minicircles of kinetoplast DNA (kDNA) networks. Using coarse-grained molecular dynamics simulations, we investigate the impact of molecular topological linkage and nanoconfinement on the conformational properties of two- and three-ring polymer systems in varying solvent qualities. Under good-quality solvents, for two-ring systems, a higher number of crossing points lead to a more internally constrained structure, reducing their mean radius of gyration...
March 21, 2024: Journal of Chemical Physics
https://read.qxmd.com/read/38507575/hierarchical-framework-for-predicting-entropies-in-bottom-up-coarse-grained-models
#16
JOURNAL ARTICLE
Jaehyeok Jin, David R Reichman
The thermodynamic entropy of coarse-grained (CG) models stands as one of the most important properties for quantifying the missing information during the CG process and for establishing transferable (or extendible) CG interactions. However, performing additional CG simulations on top of model construction often leads to significant additional computational overhead. In this work, we propose a simple hierarchical framework for predicting the thermodynamic entropies of various molecular CG systems. Our approach employs a decomposition of the CG interactions, enabling the estimation of the CG partition function and thermodynamic properties a priori...
March 20, 2024: Journal of Physical Chemistry. B
https://read.qxmd.com/read/38506294/stochastic-kinetic-theory-applied-to-coarse-grained-polymer-model
#17
JOURNAL ARTICLE
Shangren Zhu, Patrick T Underhill
A stochastic field theory approach is applied to a coarse-grained polymer model that will enable studies of polymer behavior under non-equilibrium conditions. This article is focused on the validation of the new model in comparison with explicit Langevin equation simulations under conditions with analytical solutions. The polymers are modeled as Hookean dumbbells in one dimension, without including hydrodynamic interactions and polymer-polymer interactions. Stochastic moment equations are derived from full field theory...
March 21, 2024: Journal of Chemical Physics
https://read.qxmd.com/read/38502011/effects-of-nanoparticle-wettability-on-the-meniscus-stability-of-oil-water-systems-a-coarse-grained-modeling-approach
#18
JOURNAL ARTICLE
Thao X D Nguyen, Sepideh Razavi, Dimitrios V Papavassiliou
A coarse-grained modeling approach is employed to probe the effect of nanoparticles and their wettability on the stability of the interface between two immiscible fluids. In this study, pure oil (dodecane) and water are placed side by side in a nanochannel, forming a meniscus. Homogeneous hydrophilic nanoparticles, Janus particles, and homogeneous hydrophobic nanoparticles are placed at the oil-water interface, and their dynamics are studied as they rearrange at the oil-water interface. The results show that when the water is set in motion, two instabilities occur: the formation of fingers and the detachment of water from the channel wall...
March 19, 2024: Journal of Physical Chemistry. B
https://read.qxmd.com/read/38501190/influence-of-ion-and-hydration-atmospheres-on-rna-structure-and-dynamics-insights-from-advanced-theoretical-and-computational-methods
#19
REVIEW
Raju Sarkar, Avijit Mainan, Susmita Roy
RNA, a highly charged biopolymer composed of negatively charged phosphate groups, defies electrostatic repulsion to adopt well-defined, compact structures. Hence, the presence of positively charged metal ions is crucial not only for RNA's charge neutralization, but they also coherently decorate the ion atmosphere of RNA to stabilize its compact fold. This feature article elucidates various modes of close RNA-ion interactions, with a special emphasis on Mg2+ as an outer-sphere and inner-sphere ion. Through examples, we highlight how inner-sphere chelated Mg2+ stabilizes RNA pseudoknots, while outer-sphere ions can also exert long-range electrostatic interactions, inducing groove narrowing, coaxial helical stacking, and RNA ring formation...
March 19, 2024: Chemical Communications: Chem Comm
https://read.qxmd.com/read/38498914/competition-between-stacking-and-divalent-cation-mediated-electrostatic-interactions-determines-the-conformations-of-short-dna-sequences
#20
JOURNAL ARTICLE
Balaka Mondal, Debayan Chakraborty, Naoto Hori, Hung T Nguyen, D Thirumalai
Interplay between divalent cations (Mg2+ and Ca2+ ) and single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), as well as stacking interactions, is important in nucleosome stability and phase separation in nucleic acids. Quantitative techniques accounting for ion-DNA interactions are needed to obtain insights into these and related problems. Toward this end, we created a sequence-dependent computational TIS-ION model that explicitly accounts for monovalent and divalent ions. Simulations of the rigid 24 base-pair (bp) dsDNA and flexible ssDNA sequences, dT30 and dA30 , with varying amounts of the divalent cations show that the calculated excess number of ions around the dsDNA and ssDNA agree quantitatively with ion-counting experiments...
March 18, 2024: Journal of Chemical Theory and Computation
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