Review
Chemistry, Multidisciplinary
Shukun Tang, Zahra Davoudi, Guangtian Wang, Zihao Xu, Tanzeel Rehman, Aleksander Prominski, Bozhi Tian, Kaitlin M. Bratlie, Haisheng Peng, Qun Wang
Summary: This review discusses the emergence of soft materials in synthetic biology, with a focus on biological and artificial membranes. It highlights the construction of non-native membranes and polymeric membranes for medical applications, as well as the preparation of artificial membranes using synthetic materials. By modifying artificial membranes through traditional chemical methods, such as click reactions, targeted delivery of nanocarriers and controlled release of therapeutics can be achieved. Biological membranes with active domains play a crucial role in disease targeting and inspire the development of nanocarriers with artificial membranes for complex diseases.
CHEMICAL SOCIETY REVIEWS
(2021)
Article
Biochemistry & Molecular Biology
Chloe Luyet, Paolo Elvati, Jordan Vinh, Angela Violi
Summary: A study has found a link between the mechanical properties of cellular membranes and key biological activities, which can be used for identification. The study used computational methods to simulate and compare vibrational spectra in the low-THz region for mammalian and bacterial membranes, investigating the impact of membrane asymmetry and composition, as well as conserved frequencies of specific cells. The results showed that asymmetry does not affect the vibrational spectra, and the impact of sterols depends on the mobility of membrane components. The study suggests that vibrational spectra can be used to distinguish between membranes and could be used for identifying different organisms. The method can also be applied to analyze vibrations of various biologically-relevant nanoscale structures, such as amyloid fibers, polysaccharides, and protein-ligand structures.
Article
Chemistry, Multidisciplinary
Sioned F. Jones, Himanshu Joshi, Stephen J. Terry, Jonathan R. Burns, Aleksei Aksimentiev, Ulrike S. Eggert, Stefan Howorka
Summary: Equipping DNA with hydrophobic anchors enables targeted interaction with lipid bilayers for various applications. Through experiments and molecular dynamics simulations, the study reveals the complex structure and energetics of hydrophobically tagged DNA within lipid membranes. Fundamental insight gained on DNA-bilayer interactions will guide the rational design of membrane-targeting nanostructures.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biophysics
Madhusmita Tripathy, Anand Srivastava
Summary: This study investigates the spatial and dynamic heterogeneity in mixed phase membranes and explores the relationship between membrane order, packing defects, and membrane functions. The results suggest that heterogeneity in mixed phase membranes arises from local lipid topology and its temporal evolution, leading to distinct packing and distribution of free volume in ordered and disordered domains. These packing-related basic design principles closely govern the membrane functions such as protein localization and small molecule permeability.
BIOPHYSICAL JOURNAL
(2023)
Article
Engineering, Chemical
Jincheng Lou, Mark Dudley, Jingbo Wang, Yiming Liu, Tzahi Y. Cath, Craig S. Turchi, Michael B. Heeley, Eric M. V. Hoek, David Jassby, Nils Tilton
Summary: Membrane distillation (MD) is a thermal desalination process that can increase single-pass recovery by using composite membranes with a thermally conductive layer, but this also brings challenges in lateral heat conduction through the thin membrane.
JOURNAL OF MEMBRANE SCIENCE
(2023)
Article
Chemistry, Physical
Sreetama Pal, Amitabha Chattopadhyay
Summary: Water plays a crucial role in the self-assembly of lipids and proteins into biological membranes, with the functional relevance of hydration in membrane biology still being explored. Recent research utilizing terahertz spectroscopy to study the interplay of membrane electrostatics and crowding on membrane hydration dynamics represents a significant advancement. The potential of the THz toolbox in addressing contemporary issues in membrane biology is vast and largely untapped, with an emphasis on the adaptability of the analytical framework recently reported.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Biology
Stephen Pates, Allison C. Daley, David A. Legg, Imran A. Rahman
Summary: The biological pump is crucial for transporting nutrients from surface-dwelling primary producers to deep-sea animal communities. The establishment of an efficient biological pump was likely a key factor enabling the diversification of animals over 500 million years ago during the Cambrian explosion. Vertical migration of animals is one of the main mechanisms through which the modern biological pump operates.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Engineering, Chemical
Zhenyu Zhao, Bao Liu, Ayesha Ilyas, Maarten Vanierschot, Koenraad Muylaert, Ivo F. J. Vankelecom
Summary: The use of negatively charged patterned membranes was found to be effective in harvesting microalgae, with high clean water permeance, low membrane intrinsic resistance, and high critical flux. Membrane vibration could further reduce membrane fouling. The synergistic effect between membrane structure, vibration system, and charge led to a significantly enhanced membrane performance.
JOURNAL OF MEMBRANE SCIENCE
(2021)
Review
Biotechnology & Applied Microbiology
Jiawen Niu, Chenlu Liu, Xiaopeng Yang, Wenlong Liang, Yufu Wang
Summary: Micro-nano robots have promising applications in biomedicine and the design of their motor is crucial. Living cells such as bacteria with flagella, sperm, and algal cells are commonly used as motors. Scientists have also developed biomimetic motors with functionalized cell membranes. This paper provides a comprehensive review of micro-nano robots utilizing living cells and functionalized biological cell membranes, discusses their potential practical applications, and addresses potential challenges for future development.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Physical
Katelyn M. Duncan, Rhys C. Trousdale, Cristina N. Gonzales, William H. Steel, Robert A. Walker
Summary: Time-resolved fluorescence spectroscopy in combination with differential scanning calorimetry (DSC) was used to investigate the chemical interactions of l-phenylalanine with phosphatidylcholine vesicles. The study reveals l-phenylalanine's affinity for lipid bilayers, the effects of its partitioning on bilayer properties, its solvation within the bilayer, and the quantity of l-phenylalanine in the local solvation environment. Results show that l-phenylalanine reduces the heat required to melt saturated phosphatidylcholine bilayers but does not change the transition temperature. Moreover, the study provides insights into the structure and chemistry of membrane-soluble peptides and selected membrane proteins.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Applied
Devandar Chauhan, Prashant Kumar Nagar, Kamakshi Pandey, Kamlendra Awasthi, Harsh Pandey
Summary: This review article summarizes literature on simulations of physically surface-patterned membranes and discusses the various factors affecting their anti-fouling performance, including membrane dimensions, fluid flow velocity and direction, particle size, and pattern size. The review concludes that the pattern dimensions have the most significant influence on the anti-fouling performance.
SEPARATION AND PURIFICATION REVIEWS
(2023)
Article
Biology
Pepijn Beekman, Agustin Enciso-Martinez, Sidharam P. Pujari, Leon W. M. M. Terstappen, Han Zuilhof, Severine Le Gac, Cees Otto
Summary: The study found that organosilicon compounds may interact with cell membranes passively and be adsorbed in or on the cell membrane; these compounds are commonly present in everyday items and widely used in food, cosmetics, and pharmaceuticals; with the increasing application of organosilicon compounds as replacements for other plastics, there is a need for a deeper understanding of these interactions.
COMMUNICATIONS BIOLOGY
(2021)
Article
Geochemistry & Geophysics
Xiao Gao, Jie Li, Kaiming Hu, Yanyang Zhao, Yu Han, Fang Liu, Maurice E. Tucker, Zuozhen Han
Summary: The entire process of cell membrane calcification in Bacillus licheniformis DB1-9 was studied using molecular dynamics and microbially-induced carbonate precipitation experiments. The evolution process of the calcification includes the formation of ion-pairs, multi-ion complexes, pre-nucleated clusters, amorphous calcium carbonate, and carbonate minerals. The study provides insights into microbial calcification in aquatic environments and the formation of microbialites in the geological record.
Article
Physics, Fluids & Plasmas
Marco Picchi Scardaoni
Summary: This study investigates the energetics of cell division in epithelia and highlights the interplay of key parameters regulating mitosis. It demonstrates the existence of an energetically favorable region in the parameter space, independent of cell elasticity and weakly dependent on the ratio between mother and daughter cell areas. These findings may lead to an accurate characterization of cells with anomalous proliferation.
Article
Engineering, Chemical
Moritz A. Junker, Wiebe M. de Vos, Rob G. H. Lammertink, Joris de Grooth
Summary: The study found that hollow fiber nanofiltration membranes hold potential for water treatment applications, but a better understanding of the impact of fiber dimension and operating conditions on membrane performance is needed. Through experimental research, it was observed that fiber length and operating flow velocity have a significant influence on the retention of magnesium sulfate under certain conditions.
JOURNAL OF MEMBRANE SCIENCE
(2021)
Article
Mathematical & Computational Biology
Thierry Mignon, Simon Mendez
Summary: At low shear rates, studying the dynamics of a single red blood cell in shear flow involves complex behaviors that require mathematical models and techniques from algebraic geometry. By rewriting existing models and determining steady-state solutions, a better understanding of the transition between different motions of red blood cells can be achieved.
MATHEMATICAL MODELLING OF NATURAL PHENOMENA
(2021)
Article
Biochemical Research Methods
Pierre Taraconat, Jean-Philippe Gineys, Damien Isebe, Franck Nicoud, Simon Mendez
Summary: Numerical results emphasize the link between cell flow-induced rotation and error in measured volume, leading to the development of two methods to identify and reject rotation-associated pulses. Detecting and rejecting rotation-induced pulses yield results comparable to hydrodynamical focusing, the gold standard implementation of the Coulter principle.
Article
Multidisciplinary Sciences
Thomas Puiseux, Anou Sewonu, Ramiro Moreno, Simon Mendez, Franck Nicoud
Summary: A numerical approach for simulating time-resolved 3D phase-contrast MRI under realistic flow conditions is presented. The Navier-Stokes and Bloch equations are solved with specific strategies to reduce computational cost. The simulated results compare favorably with experimental data.
Article
Physics, Fluids & Plasmas
P. Matteoli, F. Nicoud, S. Mendez
Summary: This study compares the impact of internal fluid viscosity and membrane viscosity on tank-treading red blood cells using numerical simulations supported by experimental data. It is found that both viscosities decrease the tank-treading frequency and have moderate effects on the cell deformation. Furthermore, direct inference of membrane viscosity as a function of shear rate is proposed based on the comparison between simulations and experiments.
PHYSICAL REVIEW FLUIDS
(2021)
Article
Acoustics
Yunyun Sun, Florian Vixege, Khuram Faraz, Simon Mendez, Franck Nicoud, Damien Garcia, Olivier Bernard
Summary: In this article, a numerical framework for generating clinical-like color Doppler imaging (CDI) is presented. Synthetic blood vector fields and realistic clutter artifacts are simulated for evaluating and improving the quality of Doppler imaging techniques.
IEEE TRANSACTIONS ON ULTRASONICS FERROELECTRICS AND FREQUENCY CONTROL
(2022)
Article
Engineering, Biomedical
Alain Berod, Christophe Chnafa, Simon Mendez, Franck Nicoud
Summary: Numerical computations of hemodynamics inside intracranial aneurysms treated by endovascular braided devices such as flow-diverters contribute to understanding and improving such treatment procedures. Nevertheless, these simulations yield high computational and meshing costs due to the heterogeneity of length scales between the dense weave of the fine struts of the device and the arterial volume.
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING
(2022)
Article
Engineering, Biomedical
Florian Vixege, Alain Berod, Yunyun Sun, Simon Mendez, Olivier Bernard, Nicolas Ducros, Pierre-Yves Courand, Franck Nicoud, Damien Garcia
Summary: The iVFM technique, improved with physical constraints, accurately measures blood flow velocity in the heart and shows promising potential in assessing diastolic function in clinical settings.
PHYSICS IN MEDICINE AND BIOLOGY
(2021)
Article
Engineering, Biomedical
Florian Vixege, Alain Berod, Pierre-Yves Courand, Simon Mendez, Franck Nicoud, Philippe Blanc-Benon, Didier Vray, Damien Garcia
Summary: Three-dimensional intraventricular vector flow mapping (3D-iVFM) is a method for observing the velocity vector fields of blood flow in the left ventricular cavity through three-dimensional reconstruction. By using a clinical triplane echocardiographic mode, 3D-iVFM is able to recover three-component velocity vector fields in the entire ventricular volume. Our results indicate that 3D-iVFM can accurately estimate the full-volume information of left intraventricular hemodynamics and decipher the dynamics of the intraventricular vortex during systole.
PHYSICS IN MEDICINE AND BIOLOGY
(2022)
Article
Radiology, Nuclear Medicine & Medical Imaging
Morgane Garreau, Thomas Puiseux, Solenn Toupin, Daniel Giese, Simon Mendez, Franck Nicoud, Ramiro Moreno
Summary: This study evaluated hemodynamic markers obtained by accelerated GRAPPA and compressed sensing 4D flow MRI sequences under complex flow conditions. The results showed similar hemodynamic patterns between MRI and computational fluid dynamics simulations, with larger discrepancies near the boundary walls. MRI scans tended to overestimate velocity profiles and peak velocities, but showed good agreement for flow rates. Computational fluid dynamics simulations are a useful tool to assess these differences, but are sensitive to modeling parameters.
MAGNETIC RESONANCE IN MEDICINE
(2022)
Article
Engineering, Biomedical
Franck Nicoud
Summary: An adjoint-based methodology is proposed to compute the gradient of outcomes in the coagulation cascade mathematical models. The method is validated using a simple case involving 3 species and further applied to a complex model with 34 species and 45 reactions. The results show that the method produces consistent gradient estimates at a lower computational cost compared to the finite differences approximation.
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING
(2023)
Article
Engineering, Biomedical
Alain Berod, Fernando Mut, Juan Cebral, Simon Mendez, Christophe Chnafa, Franck Nicoud
Summary: The study applies a heterogeneous model developed by Berod et al to evaluate the hemodynamic effects of endovascular prostheses on cerebral aneurysms. The model shows good agreement with the actual treatment outcomes and successfully reproduces the jetting-type flows generated downstream of the struts.
INTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING
(2023)
Article
Automation & Control Systems
Gil Marques, Marco Martins Afonso, Silvio Gama
Summary: We introduce a novel method to estimate the circulations and positions of point vortices in a 2D environment using trajectory data of passive particles affected by Gaussian noise. The method consists of two algorithms: one for calculating the vortex circulations, and the other for reconstructing the vortex trajectories. Through a hierarchy of optimization problems, involving the integration of systems of differential equations over time sub-intervals with the same amplitude defined by the autocorrelation function of the advected passive particles' trajectories, we find that accurately tracking the vortex position and determining its circulation is achievable even in the presence of noise.
IEEE CONTROL SYSTEMS LETTERS
(2023)
Article
Mechanics
S. Blanchard, N. Odier, L. Gicquel, B. Cuenot, F. Nicoud
Summary: In the framework of wall-modeled large-eddy simulation (WMLES), the static Smagorinsky model predicts efficiently the wall shear stress, while more advanced static models like WALE or Sigma fail in this aspect. Smagorinsky is known to be too dissipative in the bulk flow and purely sheared flows, whereas the other models are better suited for near-wall flows.
