Article
Biochemistry & Molecular Biology
Bengi Altintel, Burcin Acar, Burak Erman, Turkan Haliloglu
Summary: Allostery, a key biological control mechanism, can be described using dynamic information flow. This study introduces a novel approach based on the Gaussian Network Model (GNM) to dissect dynamic information and reveal multi-directional allosteric pathways in protein structures. By analyzing information transfer between residues, specific residues with high dynamic capacity are identified as potential targets for structure-based rational drug design.
JOURNAL OF MOLECULAR BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Romualdo Troisi, Nicole Balasco, Ida Autiero, Luigi Vitagliano, Filomena Sica
Summary: This study investigates the structural determinants of thrombin partnerships with various ligands, focusing on the interaction between thrombin and exosite ligands, especially the specificity of thrombin binding to aptamers. The research reveals new insights into the design of thrombin inhibitors and the interface area between thrombin and exosite ligands.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Eunjeong Lee, Matthew J. Mcleod, Jasmina S. Redzic, Barbara Marcolin, Robert E. Thorne, Pratul Agarwal, Elan Zohar Eisenmesser
Summary: Biliverdin Reductase B (BLVRB) is an NADPH-dependent reductase that undergoes structural and dynamics changes during its catalytic cycle. Through X-ray crystallography, the apo BLVRB structure was determined for the first time, revealing global changes compared to the holo structure. Amide and Ca chemical shift perturbations were used to identify environmental and secondary structural changes between intermediates, while NMR relaxation rate measurements provided insights into the dynamic behavior of BLVRB.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Jennifer Y. Cui, George P. Lisi
Summary: Cytokines play a key role in cellular communication and biological regulation. Their timing, quantity, and localization are crucial in producing specific biological outcomes. Through molecular observation, insights gained may complement a system-level understanding of cytokine biology, explaining the diversity of downstream signaling events and informing therapeutic and experimental development.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Engineering, Multidisciplinary
Bo Fang, Yilong Wang, Bingheng Zhu, Yi Wu, Yishen Tian, Youxia Li, Dengqing Cao
Summary: Due to the complexity and high degrees of freedom, dynamical modelling of ring truss antenna (RTA) is challenging. To overcome these obstacles, a dynamical modeling method named the 3D-Global Mode Method is proposed to obtain the low-dimensional analytical dynamical model of a flexible arm-supported ring antenna (ASRA) that vibrates spatially.
APPLIED MATHEMATICAL MODELLING
(2023)
Review
Biochemical Research Methods
Ammu Prasanna Kumar, Chandra S. Verma, Suryani Lukman
Summary: Rab proteins play a critical role in various diseases, and researchers have proposed a workflow involving multiple computational methods to aid future research in drug discovery targeting Rab protein allosteric sites.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Green & Sustainable Science & Technology
Tomoko Hasegawa, Shinichiro Fujimori, Stefan Frank, Florian Humpenoeder, Christoph Bertram, Jacques Despres, Laurent Drouet, Johannes Emmerling, Mykola Gusti, Mathijs Harmsen, Kimon Keramidas, Yuki Ochi, Ken Oshiro, Pedro Rochedo, Bas van Ruijven, Anique-Marie Cabardos, Andre Deppermann, Florian Fosse, Petr Havlik, Volker Krey, Alexander Popp, Roberto Schaeffer, Detlef van Vuuren, Keywan Riahi
Summary: Delaying climate mitigation leads to a need for large-scale carbon dioxide removal in the future, which may have adverse effects. This study analyzes the implications of climate mitigation scenarios that do not rely on CDR technologies for land-use and food systems, highlighting the benefits and trade-offs of early climate action and the increased risk of food insecurity in the near term.
NATURE SUSTAINABILITY
(2021)
Article
Optics
Yingning Wang, Wenqian Zhao, Jiahe Hu, Zhi Wang, Yan-Ge Liu, Changjing Bao, Yongxiong Ren, Zhongqi Pan, Yang Yue
Summary: In this letter, we propose and design a 19-ring air-core fiber that can support approximately 3000 orbital angular momentum (OAM) modes. The fiber exhibits low inter-ring cross talk and high stability, making it suitable for spatial division multiplexing (SDM) in next-generation high-speed optical communication systems.
Article
Biodiversity Conservation
Muhammed A. Oyinlola, Gabriel Reygondeau, Colette C. C. Wabnitz, Thomas L. Frolicher, Vicky W. Y. Lam, William W. L. Cheung
Summary: The sustainability of global seafood supply is facing challenges, including the risks posed by climate change to mariculture production. Projections show that future global mariculture production will be influenced by climate and socio-economic scenarios, with some countries projected to experience a decline in production potential.
GLOBAL CHANGE BIOLOGY
(2022)
Article
Acoustics
Alessandro Cammarata, Pietro Davide Maddio
Summary: This paper proposes a strategy to reduce the complexity of flexible multibody systems using global modes for reduced-order models. Compared to traditional methods, this approach involves only elastic coordinates while retaining gross motion coordinates to describe the deformation field of the mechanisms.
JOURNAL OF SOUND AND VIBRATION
(2021)
Article
Multidisciplinary Sciences
Xia Li, Guangzhao Chen, Yongping Zhang, Le Yu, Zhenrong Du, Guohua Hu, Xiaojuan Liu
Summary: Systematic studies show that there are uncertainties when using global LULC products, especially with coarser resolutions, which can distort urban features. Additionally, most of these products underestimate crop production losses.
Review
Biology
Shuli Niu, Lei Song, Jinsong Wang, Yiqi Luo, Guirui Yu
Summary: Through a literature review, it was found that nitrogen input stimulates plant primary productivity but inconsistently affects microbial activities and soil carbon sequestration. Nitrogen fixation increases and nitrogen leaching decreases under elevated CO2 and temperature or along ecosystem succession, resulting in improved soil nitrogen availability and supporting plant growth and ecosystem carbon sequestration. Ecosystem models that fail to simulate these dynamic adjustments cannot accurately predict carbon-nitrogen coupling and ecosystem carbon sequestration.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Multidisciplinary Sciences
Bernhard Lehner, Mathis L. Messager, Maartje C. Korver, Simon Linke
Summary: The LakeAT LAS dataset provides a wide range of hydro-environmental characteristics for over 1.4 million lakes and reservoirs globally, and its standardized format allows for versatile applicability in hydro-ecological assessments from regional to global scales.
Article
Multidisciplinary Sciences
Dayun Kang, Jungsoon Choi, Yeonju Kim, Donghyok Kwon
Summary: This study conducted a spatiotemporal analysis of COVID-19 cases in South Korea, revealing spatial clustering patterns and temporal variations. The initial hotspots were concentrated in Daegu and Gyeongsangbuk-do, followed by metropolitan areas. The study provides a powerful approach to understanding the spatial dynamics of COVID-19 in South Korea.
SCIENTIFIC REPORTS
(2022)
Article
Infectious Diseases
Mark F. Olson, Jose G. Juarez, Moritz U. G. Kraemer, Jane P. Messina, Gabriel L. Hamer
Summary: This study examines the association between the urban arbovirus vector Aedes aegypti and dengue virus, revealing the phenomenon of 'aegyptism without arbovirus' in different parts of the world. It explores how environmental and socioeconomic variables, such as human population density, temperature, and precipitation, influence the deviations in the probability of vector and human disease occurrence. The findings provide valuable insights for understanding and addressing the risk of arbovirus transmission in regions with established Ae. aegypti populations but low or no autochthonous transmission of human-amplified arboviruses.
PLOS NEGLECTED TROPICAL DISEASES
(2021)
Article
Neurosciences
Sarbjit Nijjar, Daniel Maddison, Louise Meigh, Elizabeth de Wolf, Thomas Rodgers, Martin J. Cann, Nicholas Dale
Summary: A moderate increase in PCO2 (55 mmHg) can close Cx26 gap junctions independently of changes in pH, relying on specific residues and a carbamylation reaction. Pathological mutations of Cx26 can abolish this CO2-dependent closing effect, which is mediated through changes in protein entropy state. The action of CO2 on Cx26 gap junctions is different from its effect on hemichannels, with opposing actions dependent on the same residues and presumed carbamylation reaction.
JOURNAL OF PHYSIOLOGY-LONDON
(2021)
Article
Physics, Multidisciplinary
Charley Schaefer, Tom C. B. McLeish
Summary: The tube model confirms analytical predictions for sticky diffusivity and shows a power law distribution of stretch in steady-state extensional flow. Strong stochastic forcing is found to be the driving factor behind the long tail of the distribution, leading to rare events of reaching a threshold stretch and offering insights into nucleation rates of flow-induced crystallization in systems of associating polymers under flow. The model also represents a wide class of driven systems with strong and scaling fluctuations.
PHYSICAL REVIEW LETTERS
(2021)
Article
Biochemistry & Molecular Biology
Charley Schaefer, Peter R. Laity, Chris Holland, Tom C. B. McLeish
Summary: The flow-induced self-assembly of entangled Bombyx mori silk proteins is hypothesized to be aided by the registration of aligned protein chains using intermolecular interacting sticky patches. Despite a clear correlation length of the stickers in the direction of the flow, there is a very broad distribution of protein-chain stretch, suggesting the registration of proteins is not directly coupled to the applied strain but may be a slow statistical process. This qualitative prediction seems to be consistent with the large strains required to induce gelation in rheological measurements under constant shear in the long time scales.
Article
Engineering, Chemical
Thomas P. John, Claudio P. Fonte, Adam Kowalski, Thomas L. Rodgers
Summary: This study comprehensively investigates the effect of impeller geometry on the relationship between power and flow in stirred vessels using a combination of angular momentum balance analysis and computational fluid dynamics simulations. The results allow for accurate prediction of the flow generated by the impeller based on easily measurable impeller power consumption and geometrical dimensions. The models are accurate over a wide range of geometries and can predict both primary and total flows.
Article
Chemistry, Physical
Mitha Al-Jabri, Thomas Rodgers
Summary: Formulated products are essential in our daily life and often contain common components like oil, water, particles, and surfactants. The main aim of this study is to gain further insight into surfactant dissolution process by changing the concentration and hydrophobicity of surfactants. Results indicate that higher hydrophobicity of surfactants results in the formation of elongated worm-like micelles, while lower hydrophobicity produces spherical micelles, during the dissolution process.
Correction
Multidisciplinary Sciences
Franca Davenport, Martin J. Cann, Stephen Smye, Tom McLeish
Article
Mechanics
Charley Schaefer, Tom C. B. McLeish
Summary: Silk, a semidilute solution of associating polypeptide chains, crystallizes under stretch-induced disruption in strong extensional flow. Simulations and calculations show that the associations hinder chain alignment but facilitate stretching at low specific work. The chemical tunability of associations in silkworms optimizes chain alignment and stretching in different locations along the spinning duct, highlighting the potential advantages of chemically tunable processing of synthetic association polymers for biomimetic industrial purposes.
JOURNAL OF RHEOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Lynsay Blake, Martin J. Cann
Summary: Carbon dioxide plays a crucial role in various life processes, regulating cellular reactions, transport, maintenance, and behavior. Protein carbamate modification, mediated by carbon dioxide, is a mechanism that may alter protein function and participate in sensing and signaling.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Multidisciplinary Sciences
Alejandra Guillen-Garcia, Savannah E. R. Gibson, Caleb J. C. Jordan, Venkata K. Ramaswamy, Victoria L. Linthwaite, Elizabeth H. C. Bromley, Adrian P. Brown, David R. W. Hodgson, Tim R. Blower, Jan R. R. Verlet, Matteo T. Degiacomi, Lars-Olof Palsson, Martin J. Cann
Summary: CO2 regulates electronic energy transfer in cyanobacteria by binding to and enhancing the activity of the light-harvesting complex. This finding provides important insights into the regulation of photosynthesis.
NATURE COMMUNICATIONS
(2022)
Article
Instruments & Instrumentation
Carolina Cruz, Ali Arafeh, Philip A. A. Martin, Claudio P. Fonte, Antonio De Simone, Felix K. K. Oppong, Will Jeatt, Thomas L. L. Rodgers
Summary: This study focuses on using near-infrared (NIR) and Raman spectroscopy as analytical tools to assess the viscosity of ice cream mixes. The results suggest that NIR spectroscopy performs better than Raman spectroscopy in predicting viscosity. However, other factors should also be considered when choosing the best method.
APPLIED SPECTROSCOPY
(2023)
Article
Chemistry, Physical
Mitha Al-Jabri, Thomas Rodgers
Summary: The purpose of this study is to investigate the impact of surfactant chain length and hydrophobic to hydrophilic ratio on the dissolution process. The results show that increasing the length of the hydrophobic part slows down the dissolution process, while increasing the length of the hydrophilic part speeds it up. However, the effect of adding more hydrophobic beads is greater than that of adding more hydrophilic beads on the dissolution process.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Engineering, Chemical
Carolina Cruz, Claudio P. Fonte, Antonio De Simone, Felix K. Oppong, Will Jeatt, Thomas L. Rodgers
Summary: Three analytical tools were investigated for characterizing ice fraction and viscosity of water ices, namely conductivity, torque measurements, and near-infrared spectroscopy (NIR). A predictive model using conductivity measurements was developed for ice fraction analysis of sucrose water ices with Csuc >= 25 wt.%. Although the model only provided a rough estimation of ice quantity due to instrument limitations, further studies are warranted to explore its potential. The increase in ice fraction was found to be related to the increase in viscosity, as determined by torque measurements. An empirical model describing the viscosity evolution with ice fraction showed a strong correlation (R2=0.986). NIR spectroscopy was not suitable for ice fraction analysis in this study, but it has been utilized by other researchers for characterizing ice cream mixes, including rheological properties.
JOURNAL OF FOOD ENGINEERING
(2023)
Article
Education, Scientific Disciplines
Thomas L. Rodgers, Philip Bolton, Percy van der Gryp
Summary: This paper presents a set of interactive graphs for teaching chemical engineering topics and explores students' opinions and motivations for using these graphs. The findings demonstrate that the use of online interactive graphs is popular among students, with performance expectancy and hedonic motivation being the main driving factors.
EDUCATION FOR CHEMICAL ENGINEERS
(2023)
Article
Engineering, Chemical
Yuqi Bai, Claudio Pereira Fonte, Adam Kowalski, Waldo Rosales-Trujillo, Thomas Lawrence Rodgers
Summary: A general methodology for characterising stirred tank mixers using two-dimensional network-of-zones (2-D NoZ) model was introduced in this work. Starting from high resolution 3-D velocity field database such as CFD simulations, flow patterns were preserved and simplified into 2-D inter-zonal flowrates and mass imbalances were corrected in the defined routine. Mixing time estimation and turbulent dissipation rate profiles were chosen as metrics for evaluation of the generated 2-D NoZ model, which were compared to CFD passive scalar and literature results on two typical stirred tank geometries covering both radial flow and axial flow impellers.
CHEMICAL ENGINEERING RESEARCH & DESIGN
(2023)
Article
Biology
Victoria L. Linthwaite, Martin J. Cann
Summary: Carbon dioxide can influence cell phenotypes through modulating signalling pathways and regulating various cellular processes. The carbamate post-translational modification (PTM) on proteins, formed by CO2 interacting with neutral amines, may be more widespread in biology than previously thought, suggesting it as a broadly relevant mechanism for CO2-protein interactions.