Article
Mechanics
Duan Z. Zhang
Summary: This study establishes a relationship between ensemble average and nearest particle statistics to study long-range particle interactions and calculate particle sedimentation velocity. Additionally, it introduces an important particle-fluid-particle stress for general multiphase flows.
JOURNAL OF FLUID MECHANICS
(2021)
Review
Biochemical Research Methods
Shaofeng Liao, Yujun Zhang, Yifei Qi, Zhuqing Zhang
Summary: Liquid-liquid phase separation (LLPS) of proteins and nucleic acids is crucial for the formation of biomolecular condensates in cells. Dysregulation of protein LLPS is associated with various difficult-to-treat diseases. Several tools have been developed to predict phase-separating proteins (PSPs) using different algorithms and datasets. In this study, we evaluated eleven PSPs predictors and found that FuzDrop, DeePhase, and PSPredictor performed well on folded proteins, while LLPhyScore was the best predictor for the human proteome. However, none of the predictors accurately identified experimentally verified non-PSPs. More diverse training sequences and the consideration of refined sequence patterns reflecting molecular interactions may improve the performance of PSPs prediction.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Mechanics
Cheng-Hsien Lee
Summary: This study developed a multiphase model with a novel evolution equation to address the issues of shear-induced volume change and pore-pressure feedback in submarine granular flows simulated using an Eulerian-Eulerian two-phase model. The evolution equation effectively describes the relaxation process of static solid pressure and shear-induced volume change, allowing the model to capture phenomena such as time delays in initiating flows and different collapse processes for differently packed columns.
JOURNAL OF FLUID MECHANICS
(2021)
Article
Biochemical Research Methods
Xiaoquan Chu, Tanlin Sun, Qian Li, Youjun Xu, Zhuqing Zhang, Luhua Lai, Jianfeng Pei
Summary: A sequence-based prediction tool for LLPS proteins (PSPredictor) was developed with a machine learning algorithm, achieving an accuracy of 94.71% in tenfold cross-validation and outperforming previously reported PSPs prediction tools. A user-friendly PSPredictor web server was built for predicting potential PSPs.
BMC BIOINFORMATICS
(2022)
Article
Mechanics
S. Beetham, R. O. Fox, J. Capecelatro
Summary: In this study, model closures for multiphase Reynolds-averaged Navier-Stokes (RANS) equations are developed using sparse regression and Eulerian-Lagrangian simulations to ensure accuracy and robustness of the models across different flow conditions. The focus is on capturing the dynamics of gas-particle flows, particularly the generation of particle clusters and interphase momentum exchange, in a compact and algebraic manner.
JOURNAL OF FLUID MECHANICS
(2021)
Article
Mechanics
Yanbiao Gan, Aiguo Xu, Huilin Lai, Wei Li, Guanglan Sun, Sauro Succi
Summary: This paper aims to formulate and validate a multi-scale discrete Boltzmann method based on density functional kinetic theory for thermal multiphase flow systems. It also provides new insights into the thermo-hydrodynamic non-equilibrium effects in the phase separation process.
JOURNAL OF FLUID MECHANICS
(2022)
Article
Physics, Applied
Binzhen Zhang, Yangyang Wang, Yunpeng Liu, Huan Li, Wenxuan Zang, Junping Duan
Summary: This paper proposes a novel focusing method using microfilters and interdigital electrodes to capture and separate particles. Experimental results show that the capture efficiency of the chip reaches 71%-86% and the separation efficiency is over 98.6%, making it potentially suitable for separating circulating tumor cells in blood samples.
JOURNAL OF PHYSICS D-APPLIED PHYSICS
(2021)
Article
Engineering, Environmental
Katie Cole, Pablo R. Brito-Parada, Kathryn Hadler, Diego Mesa, Stephen J. Neethling, Alexander M. Norori-McCormac, Jan J. Cilliers
Summary: This study measured the hydrodynamics of a stirred tank reactor containing multiphase flows using positron emission particle tracking (PEPT) technique. The probability density function (PDF) of particle velocity was estimated by averaging the location data from PEPT. The results showed bimodal vertical velocity distributions in the impeller radial jet. Comparisons of velocity distributions between hydrophilic and hydrophobic tracer particles revealed differences in various locations.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Chemistry, Multidisciplinary
Shi Yang, Han Yu, Xiuli Xu, Ting Yang, Yue Wei, Rui Zan, Xiaonong Zhang, Qingming Ma, Ho Cheung Shum, Yang Song
Summary: This article presents the synthesis of a peptide-based RNA sensor by connecting aggregation-induced emission luminogen (AIEgen) tetraphenylethylene (TPE) to tandem peptide repeats of (RRASL)n (n = 1, 2, 3). The conjugation of TPE promotes liquid-liquid phase separation of the peptide repeats, with significantly decreased minimum coacervation concentration (MCC) compared to the untagged counterparts. Furthermore, the luminescence of TPE-(RRASL)n is greatly enhanced with increasing RNA concentration, attributed to the constricted rotation of the TPE moiety within the droplet phase formed by peptide/RNA coacervates. In addition, TPE-(RRASL)n can efficiently penetrate human gallbladder carcinoma cells, translocate into the nucleus, and colocalize with intracellular RNA, highlighting its potential as a droplet-based biosensor for intracellular RNA imaging.
Article
Mechanics
Y. Mezui, M. Obligado, A. Cartellier
Summary: The hydrodynamics of bubble columns in the heterogeneous regime is studied experimentally. The void fraction field at small scales is analyzed and found to differ significantly from a random Poisson process in the heterogeneous regime. Meso-scale structures, such as clusters, void regions, and intermediate regions, are identified and found to drive the motion of bubbles. The relative velocity of bubbles is related to the concentration and characteristic size of these meso-scale structures, and a cartoon of the internal flow structure is proposed based on their values at large gas superficial velocities.
JOURNAL OF FLUID MECHANICS
(2023)
Article
Chemistry, Multidisciplinary
Yue Sun, Xiaojie Xu, Liwei Chen, Wei Leong Chew, Yuan Ping, Ali Miserez
Summary: CRISPR/Cas9-based genome editing tools have great potential for developing various therapeutic treatments. However, the efficient intracellular delivery of the editing machinery is a challenge. This study utilized a phase-separating peptide with intracellular redox-triggered release properties to encapsulate and deliver all three forms of CRISPR/Cas9 editing machinery, resulting in higher transfection and editing efficiency compared to commercially available transfection reagents.
Article
Mechanics
Amelie Ferran, Nathanael Machicoane, Alberto Aliseda, Martin Obligado
Summary: We conducted an experimental study on the gravitational settling velocity of dense, sub-Kolmogorov inertial particles in different turbulent flow conditions. Using a phase Doppler particle analyzer, we measured the settling velocity of micrometer-sized water droplets in a low-speed wind tunnel. We explored a wide range of turbulence parameters, including Reynolds numbers, Rouse numbers, and volume fractions, to analyze the effects on particle settling velocity.
JOURNAL OF FLUID MECHANICS
(2023)
Article
Engineering, Multidisciplinary
Xiangwei Dong, Guannan Hao, Ran Yu
Summary: This study uses the smoothed particle hydrodynamics (SPH) method to simulate heat transfer and phase change in multiphase media. The model incorporates a multiphase SPH model to simulate interface behavior and a thermal dynamics model to incorporate solid-liquid phase change. The numerical model is validated using benchmark examples and successfully reproduces the behavior of melted liquids at interfaces and the formation of melted droplets.
ENGINEERING APPLICATIONS OF COMPUTATIONAL FLUID MECHANICS
(2022)
Article
Engineering, Environmental
Chen Zhu, Fangfang Li, Jun Zhang, Lianzheng Zhang, Jun Gao, Yixin Ma, Dongmei Xu, Yinglong Wang
Summary: Ionic liquids with double chemical sites were designed for the separation of phenolic compounds, where both anions and cations play important roles in the separation process. Experimental data was correlated using a NRTL model to provide basic parameters for extraction process design.
JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING
(2021)
Article
Mechanics
Naveen Rohilla, Partha S. Goswami
Summary: This article explores the variation of local isotropy of fluid fluctuations and the decrease of the Kolmogorov constant in particle-laden turbulent channel flows. The author also adopts a new modeling technique using large-eddy simulation (LES) to predict fluid phase statistics without solving simultaneous particle phase equations. This study provides insights into the phenomena of drastic collapse in turbulence intensity.
JOURNAL OF FLUID MECHANICS
(2023)
Article
Biochemical Research Methods
Oliver K. Castell, Patricia M. Dijkman, Daniel N. Wiseman, Alan D. Goddard
Article
Multidisciplinary Sciences
Patricia M. Dijkman, Oliver K. Castell, Alan D. Goddard, Juan C. Munoz-Garcia, Chris de Graaf, Mark I. Wallace, Anthony Watts
NATURE COMMUNICATIONS
(2018)
Article
Pharmacology & Pharmacy
Colin Dillon, Helen Hughes, Niall J. O. Reilly, Chris J. Allender, David A. Barrow, Peter McLoughlin
INTERNATIONAL JOURNAL OF PHARMACEUTICS
(2019)
Article
Biochemical Research Methods
Suzanne K. Thomas, W. David Jamieson, Rebecca E. A. Gwyther, Benjamin J. Bowen, Adam Beachey, Harley L. Worthy, J. Emyr Macdonald, Martin Elliott, Oliver K. Castell, D. Dafydd Jones
BIOCONJUGATE CHEMISTRY
(2020)
Article
Chemistry, Multidisciplinary
Jin Li, Divesh Kamal Baxani, William David Jamieson, Wen Xu, Victoria Garcia Rocha, David Anthony Barrow, Oliver Kieran Castell
Article
Multidisciplinary Sciences
Patrick Hardinge, Divesh K. Baxani, Thomas McCloy, James A. H. Murray, Oliver K. Castell
SCIENTIFIC REPORTS
(2020)
Article
Chemistry, Multidisciplinary
Jacob R. Pope, Rachel L. Johnson, W. David Jamieson, Harley L. Worthy, Senthilkumar Kailasam, Rochelle D. Ahmed, Ismail Taban, Husam Sabah Auhim, Daniel W. Watkins, Pierre J. Rizkallah, Oliver K. Castell, D. Dafydd Jones
Summary: Fluorescent proteins (FPs) are often used in pairs to monitor biomolecular events. GFP homodimers are brighter than monomers, while heterodimers typically have lower FRET efficiency than predicted.
Correction
Multidisciplinary Sciences
Patrick Hardinge, Divesh K. Baxani, Thomas McCloy, James A. H. Murray, Oliver K. Castell
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Jin Li, William D. Jamieson, Pantelitsa Dimitriou, Wen Xu, Paul Rohde, Boris Martinac, Matthew Baker, Bruce W. Drinkwater, Oliver K. Castell, David A. Barrow
Summary: Engineering micro-emulsion is crucial for creating bottom-up synthetic cells. In this study, a droplet laboratory platform using microfluidics and acoustic levitation was developed to control membrane protein gating in functional artificial cells. The platform allows the engineering of complex emulsion-based, multicompartment artificial cells and offers the possibility of non-contact control of membrane protein function.
NATURE COMMUNICATIONS
(2022)
Article
Materials Science, Multidisciplinary
Ahmad Moukachar, Katie Harvey, Eva Roke, Katherine Sloan, Cameron Pool, Shabbir Moola, Ameer Alshukri, Danielle Jarvis, Phoebe Crews-Rees, Grace McDermott, Lluan Evans, Jin Li, Christopher Thomas, Sion Coulman, Oliver Castell
Summary: The development of low-cost accessible technologies for rapid prototyping of mechanical components has made engineering tools more accessible to hobbyists and researchers. A similar approach can be applied to the fabrication of soft-matter and biologically compatible materials, enabling advancements in biological research.
ADVANCED MATERIALS TECHNOLOGIES
(2023)
Article
Chemistry, Physical
D. K. Baxani, W. D. Jamieson, D. A. Barrow, O. K. Castell
Summary: In this study, a high-throughput membrane platform was developed using droplet bilayers encapsulated within a hydrogel shell. Through concentration screening and electrophysiology experiments, maximal activity enhancement at specific peptide concentrations and low conductance pore activity were revealed.
Meeting Abstract
Biophysics
Andrew R. Mason, William D. Jamieson, Oliver Williams, Daniel Slocombe, Oliver K. Castell
BIOPHYSICAL JOURNAL
(2020)
Correction
Chemistry, Multidisciplinary
Harley L. Worthy, Husam Sabah Auhim, W. David Jamieson, Jacob R. Pope, Aaron Wall, Robert Batchelor, Rachel L. Johnson, Daniel W. Watkins, Pierre Rizkallah, Oliver K. Castell, D. Dafydd Jones
COMMUNICATIONS CHEMISTRY
(2019)
Article
Chemistry, Multidisciplinary
Harley L. Worthy, Husam Sabah Auhim, W. David Jamieson, Jacob R. Pope, Aaron Wall, Robert Batchelor, Rachel L. Johnson, Daniel W. Watkins, Pierre Rizkallah, Oliver K. Castell, D. Dafydd Jones
COMMUNICATIONS CHEMISTRY
(2019)
Meeting Abstract
Biophysics
Divesh K. Baxani, William D. Jamieson, David A. Barrow, Oliver K. Castell
BIOPHYSICAL JOURNAL
(2018)