Article
Engineering, Chemical
Hongwei Cui, S. Saleem, Jafar Eskandari Jam, Mohsen Heydari Beni, Maboud Hekmatifar, Davood Toghraie, Roozbeh Sabetvand
Summary: The research utilized molecular dynamics simulation to investigate the effect of metallic nanoparticles on the phase transition of atomic fluid, with the addition of copper nanoparticles improving the thermal behavior of the base fluid. Results showed that simulated structures reach equilibrium after 2,000,000 time steps, and the introduction of atomic barriers increased the heat flux, leading to more fluid particles exhibiting phase phenomena.
JOURNAL OF THE TAIWAN INSTITUTE OF CHEMICAL ENGINEERS
(2021)
Article
Chemistry, Multidisciplinary
Zhixuan Zhong, Guanqun Du, Yilin Wang, Jian Jiang
Summary: Dialkyldimethylammonium bromide (2C(n)Br) surfactants in bilayer exhibit polymorphic phases and rich self-assembly behaviors. The effects of alkyl chain length on the phase behavior of the 2C(n)Br bilayer are investigated by molecular dynamics simulations. The results show that different alkyl chain lengths result in different phase structures and properties of the bilayer membranes.
Article
Chemistry, Multidisciplinary
Vivien Walter, Celine Ruscher, Olivier Benzerara, Fabrice Thalmann
Summary: MLLPA is a Python 3 module that utilizes machine learning tools to analyze lipid membrane phase domains, capable of reading various formats and models of simulation data, and suitable for studying membranes of different geometries.
JOURNAL OF COMPUTATIONAL CHEMISTRY
(2021)
Article
Chemistry, Physical
E. J. Smith, A. D. J. Haymet
Summary: The ability of antifreeze proteins and glycoproteins to prevent damage to biological membranes under cold stress is well established, but the exact mechanism of membrane stabilization is still not well understood. In this study, molecular dynamics simulations were conducted to investigate the interaction between a specific antifreeze protein and a lipid bilayer, exploring the location and mode of protein-membrane interaction as well as relevant properties for membrane stabilization.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Biochemistry & Molecular Biology
Isaac K. Asare, Alberto Perez Galende, Andres Bastidas Garcia, Mateo Fernandez Cruz, Anna Clara Miranda Moura, Conner C. Campbell, Matthew Scheyer, John Paul Alao, Steve Alston, Andrea N. Kravats, Charles R. Sanders, Gary A. Lorigan, Indra D. Sahu
Summary: This study examined the structural dynamics of KCNE3 in different lipid environments using molecular dynamics simulations. The results showed that the transmembrane domain of KCNE3 is more stable, while the N- and C-termini exhibit different levels of flexibility in various lipid conditions. The study also determined the specific locations of KCNE3 within the lipid membrane.
Article
Biochemistry & Molecular Biology
Vivien Walter, Celine Ruscher, Adrien Gola, Carlos M. Marques, Olivier Benzerara, Fabrice Thalmann
Summary: Atomistic molecular dynamics simulations have advanced to a level where they can investigate the lipid polymorphism of model bilayers at various temperatures, but may still struggle to accurately describe certain phases. Simulations on lipid bilayers of different sizes have shown that large systems may exhibit unexpected structural phases influenced by thermal history and preparation conditions. A mechanism for the observed topographic instability has been proposed.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2021)
Article
Engineering, Multidisciplinary
Yonggui Wang, Jiandong Zheng, Ghassan Fadhil Smaisim, Davood Toghraie
Summary: This study investigates the impact of CuO nanoparticles on the atomic conduct and phase transition duration of water-based fluid in a nanochannel. The results indicate that adding CuO nanoparticles reduces the phase transition duration, and the effect becomes more pronounced with increasing nanoparticle length.
ALEXANDRIA ENGINEERING JOURNAL
(2022)
Article
Biochemistry & Molecular Biology
Pengzhen Zhang, Fangfang Jiao, Lingxiao Wu, Zhe Kong, Wei Hu, Lijun Liang, Yongjun Zhang
Summary: This study investigates the permeation mechanisms of graphene quantum dots (GQDs) through different cell membranes using molecular dynamics simulations. The results show that GQDs can easily penetrate lipid membranes with low phospholipid molecule densities, but are unable to penetrate those with high densities. The study provides insights into the transmembrane transport of GQDs.
Article
Thermodynamics
Kaifeng Chen, Kunrong Zeng, Roozbeh Sabetvand
Summary: The research investigates phase transition in aluminum hydride nanoparticles coated with different atomic structures using the molecular dynamics method. The results show that nanoparticles have an impact on heat flux, phase transition time, and atomic stability time.
INTERNATIONAL COMMUNICATIONS IN HEAT AND MASS TRANSFER
(2021)
Article
Biochemistry & Molecular Biology
Shan Zhang, Ming Ma, Zhuang Shao, Jincheng Zhang, Lei Fu, Xiangyuan Li, Weihai Fang, Lianghui Gao
Summary: Temporins are a family of antimicrobial peptides isolated from frog skin, which are very short, weakly charged, and highly hydrophobic. They execute bactericidal activities by folding into α-helices at the membrane surface, extracting lipids, and forming protrusions at high peptide concentrations. These unique antimicrobial mechanisms include lipid extraction and tubule-like protrusion formation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Maria C. Oliveira, Maksudbek Yusupov, Annemie Bogaerts, Rodrigo M. Cordeiro
Summary: This study investigates the distribution of lipid aldehydes (LAs) in phase-separated membranes (PSMs) and finds that LAs derived from mono-unsaturated lipids accumulate at the interface between liquid-ordered/liquid-disordered domains, while LAs derived from poly-unsaturated lipids remain in the liquid-disordered domain. These findings are important for understanding the effects of oxidized lipids on membrane structure, properties, and organization.
ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS
(2022)
Article
Chemistry, Physical
Zsofia B. Rozsa, Balazs Fabian, Gyorgy Hantal, Milan Szori, Pal Jedlovszky
Summary: Molecular dynamics simulations have revealed that xenon, a general anaesthetic, can cause the expansion of the dipalmitoylphosphatidylcholine (DPPC) membrane, increase the membrane volume, and enhance the lateral diffusion coefficient of lipid molecules. These changes are reversed by pressure, providing insights into the molecular mechanism of general anesthesia. However, the model used does not fully account for the effects of polarizability, thus underestimating the real effect of xenon.
JOURNAL OF MOLECULAR LIQUIDS
(2023)
Article
Biochemistry & Molecular Biology
Harini Krishnan, Bishal Basak, Vaisaly R. Nath, Shirish Mishra, Padinjat Raghu
Summary: In this study, the structure of the RDGB-VAP complex at the ER-PM contact site was predicted using in-silico integrative modelling. The study identified important structural features of the RDGB protein for its localization at the contact site and revealed the significance of lysine residues in the C-terminal helix of the LNS2 domain and an unstructured region immediately c-terminal to the PITP domain for protein interaction. The model provides an explanation for the topology of the RDGB-VAP complex and sets the stage for further analysis of lipid transfer function in this setting.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Engineering, Mechanical
Haiming Lu, Yao Tang, Xunuo Cao, Panpan Zhu, Weifeng Zou, Tiefeng Li, Rui Xiao, Haofei Zhou
Summary: This study investigates the change in glass transition temperature (Tg) under different stress states in amorphous materials using molecular dynamics simulations. A theoretical model based on the free volume theory and Eyring model is proposed to quantify the stress dependence of Tg. The potential applications of tuning Tg through external stress and the sensitivity of Tg to hydrostatic and shear stresses are discussed.
EXTREME MECHANICS LETTERS
(2023)
Article
Biochemistry & Molecular Biology
Selcan Karaz, Mertcan Han, Gizem Akay, Asim Onal, Sedat Nizamoglu, Seda Kizilel, Erkan Senses
Summary: Understanding the interaction between biological membranes and extracellular matrices is crucial for controlling cell behavior and functions. This study investigates how the viscoelastic extracellular environment modifies the dynamics of lipid membranes. The results show a dynamic coupling between polymer chains and phospholipid bilayers, with the lipid bilayer viscosity directly influenced by the relaxation of the whole chain.
Article
Chemistry, Multidisciplinary
Yong Chen, Chen Chen, Amadeu K. Sum
Summary: Through systematic molecular dynamic simulations, this study provides detailed insights into the nucleation and crystal growth mechanism of mixed type II clathrate structures, revealing uncorrelated uptake rates of methane and propane molecules in different solution compositions. The coexistence of type I and type II structures in the solid phase has been captured, indicating that type I patterns appear earlier than thermodynamically preferred type II structures.
CRYSTAL GROWTH & DESIGN
(2021)
Article
Engineering, Chemical
Jeong-Hoon Sa, Amadeu K. Sum
Summary: The newly developed rock-flow cell is demonstrated to be a more robust testing tool for LDHI-AA qualification, providing advantages in visualization and quantification of hydrate formation and accumulation compared to the traditional rocking cell. It offers a closer representation of shear, phase dispersion, and flow regime in flowlines, making it more suitable for assessing hydrate slurry in oil/gas production systems.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2021)
Correction
Chemistry, Multidisciplinary
Fernando de Azevedo Medeiros, Iuri Soter Viana Segtovich, Frederico Wanderley Tavares, Amadeu K. Sum
Article
Energy & Fuels
Guangchun Song, Yuxing Li, Amadeu K. Sum
Summary: This study systematically analyzed the thermal properties of hydrate deposits formed on pipe walls, revealing their insulating effects and potential for blockages in oil and gas production flowlines. By conducting experiments and calculations on the hydrate deposit thickness and thermal conductivity, valuable insights were gained for managing hydrates in deadlegs and flowlines.
Editorial Material
Thermodynamics
Amadeu Sum, Jianwen Jiang
FLUID PHASE EQUILIBRIA
(2021)
Article
Energy & Fuels
Gustavo A. B. Sandoval, Marcio Couto Ozorio, Monica F. Naccache, Paulo R. de Souza Mendes, Amadeu K. Sum, Leandro Valim, Adriana Teixeira
Summary: This work presents a rheological analysis of cyclopentane hydrates formed in water-in-oil emulsions, investigating the influence of parameters such as pretreatment temperatures and cooling/heating rates. The study shows that the resulting hydrate slurry exhibits elasticity and shear thinning behavior, likely caused by breakdown of hydrate structures and alignment of hydrate agglomerates to the flow.
Article
Energy & Fuels
Mucong Zi, Xianwei Zhang, Luqman Mahir, Khalid Mateen, Thierry Palermo, Amadeu K. Sum
Summary: Wax deposition is a common flow assurance issue in oil/gas production and transportation, and can be measured and characterized using a new experimental system. The study finds that the deposition process involves time variation and different mechanisms.
Article
Energy & Fuels
Celina Kakitani, Daniela C. Marques, Adriana Teixeira, Leandro Valim, Moises A. Marcelino Neto, Amadeu K. Sum, Rigoberto E. M. Morales
Summary: This study focused on identifying parameters that influence hydrate formation in shut-in and restart conditions in offshore oil production. Results showed that shear rate and subcooling are key parameters, and the addition of anti-agglomerant reduces water-oil interfacial tension, promoting water/hydrate dispersion.
Article
Engineering, Chemical
Daniela C. Marques, Carlos L. Bassani, Celina Kakitani, Moises A. Marcelino Neto, Amadeu K. Sum, Rigoberto E. M. Morales
Summary: Measurements of gas hydrate deposition under sheared conditions are analyzed in this study. The experiments focus on methane hydrates and methane-ethane mixtures, examining wall deposition and gas consumption during hydrate formation, and providing mathematical insights.
INDUSTRIAL & ENGINEERING CHEMISTRY RESEARCH
(2022)
Article
Energy & Fuels
Wonjung Choi, Junghoon Mok, Jonghyuk Lee, Yohan Lee, Jaehyoung Lee, Amadeu K. Sum, Yongwon Seo
Summary: In this study, the guest exchange behaviors in hydrate-bearing sediment during depressurization-assisted replacement were experimentally investigated. The results showed that the replacement efficiency and CH4 production rate were significantly enhanced through depressurization-assisted replacement. Additionally, a larger amount of CO2 could be stored in the hydrate-bearing sediment.
Article
Energy & Fuels
Yohan Lee, Taras Y. Makogon, Amadeu K. Sum
Summary: In this study, the growth of hydrate deposits from water-saturated gas in a vertical pipe system under temperature and pressure conditions representative of a well shutdown was investigated. The study found that gas convection and water condensation affect the growth rate and morphology of hydrate deposits.
Article
Chemistry, Physical
Yong Chen, Satoshi Takeya, Amadeu K. Sum
Summary: This study reports the observation of a hidden clathrate structure, the tetragonal structure (TS-I), in gas hydrates. The TS-I forms as a cocrystal when two or more sI crystal grains with different growth directions come into contact or when the growth of an sI crystal encounters geometrical frustration. The results imply that TS-I may play an important role in the combination and/or transition between sI and sII.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Multidisciplinary Sciences
Yong Chen, Satoshi Takeya, Amadeu K. Sum
Summary: Clathrate hydrates are ordered structures stabilized by hydrophobic interactions between water and guest molecules. In this study, an alternative method is proposed to understand the complex structures of clathrate hydrates, revealing the diverse crystalline hydrogen-bonded networks that can be formed. The topological dual relations between clathrate hydrate networks and tetrahedrally close-packed structures provide insights into their nucleation, phase transition, and co-existence mechanisms. Molecular dynamics simulations are employed to explore the intrinsic structural relationships of clathrate hydrates and other unrelated ordered materials.
NATURE COMMUNICATIONS
(2023)
Article
Energy & Fuels
Yohan Lee, Taras Y. Makogon, Amadeu K. Sum
Summary: In this study, the deposition kinetics and morphology of methane hydrates were investigated at 10 MPa. It was found that non-volatile thermodynamic hydrate inhibitors (THIs) were ineffective in preventing hydrate formation near the wellhead, while volatile THIs could prevent hydrate deposition even under cold conditions. However, volatile THIs only delayed the growth of hydrate deposits in warm wellheads. The study provides insight into better management strategies for THI usage to mitigate hydrate blockage risk near the wellhead.
Article
Energy & Fuels
Ana C. G. A. Rebello, Gustavo A. B. Sandoval, Monica F. Naccache, Paulo R. de Souza Mendes, Amadeu K. Sum, Adriana Teixeira, Leandro Valim
Summary: This research investigates the formation of ethane gas hydrates in water-in-model oil emulsions. The results show that increasing the subcooling, water cut, and shear rate can reduce the induction period of the hydrates. The amount of water converted to hydrate can be estimated by analyzing the viscosity and pressure curves.
GEOENERGY SCIENCE AND ENGINEERING
(2023)
Article
Biochemistry & Molecular Biology
Philipp Grad, Katarina Edwards, Lars Gedda, Victor Agmo Hernandez
Summary: This study investigates the effects of polyethylene glycol-(PEG) modified lipids and gangliosides on the Ca2+ induced interaction between liposomes composed of palmitoyl-oleoyl phosphatidylethanolamine (POPE) and palmitoyl-oleoyl phosphatidylserine (POPS) at physiological ionic strength. The results show that naked liposomes tend to adhere, rupture, and collapse on each other's surfaces upon addition of Ca2+, eventually resulting in the formation of large multilamellar aggregates and bilayer sheets. However, the presence of gangliosides or PEGylated lipids leads to the formation of small, long-lived bilayer fragments/disks. PEGylated lipids seem to be more effective than gangliosides at stabilizing these structures. The study suggests that direct liposome-liposome fusion is not the dominating process triggered by Ca2+ in the systems studied.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Saurabh Saraswat, Archana Chugh
Summary: Cell penetrating peptides (CPP) are important tools for intracellular delivery of molecules. In this study, a novel marine-derived CPP from Engraulis japonicus, called Engraulisin, was reported. Engraulisin demonstrated successful cellular uptake and selective antimicrobial activity against Methicillin-resistant Staphylococcus aureus (MRSA), making it a potential candidate for drug delivery.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Emanuela Efodili, Ashlynn Knight, Maryem Mirza, Cedric Briones, Il-Hyung Lee
Summary: This study demonstrates the spontaneous transfer of small membrane-bound peptides between a supported lipid bilayer and giant unilamellar vesicles in vitro. The transfer occurs through the formation of hemi-fusion stalks and is limited to small peptides due to the highly curved structure of the stalk. This system provides a synthetic platform for studying peptide trafficking between synthetic membranes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Yueqi Niu, Si Jia Chen, Jeffery B. Klauda
Summary: Macrophage membranes in the activated state are more tightly packed, exhibit increased chain order across lipid species, and form specific lipid clusters. These findings provide physiologically accurate models for future computational studies of macrophage membranes and their proteins.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Niki Baccile, Vincent Chaleix, Ingo Hoffmann
Summary: This study measured the bending rigidity of self-assembled structures formed by a new biobased glucolipid bioamphiphile using neutron spin-echo (NSE) technology. The results showed that the bending rigidity of these structures is lower or higher compared to phospholipid membranes, providing a new theoretical basis for the application of these new molecular systems.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Alain Bolano Alvares, Pablo E. A. Rodriguez, Gerardo D. Fidelio
Summary: The behavior of amphiphilic molecules at the air/water interface was studied to evaluate the arrangement formed in a confined area. The surface properties of zwitterionic DPPC lipid and A beta(1-40) amyloid peptide in mixed films were investigated at different temperatures. DPPC undergoes a phase transition depending on temperature and lateral pressure, which allows for the study of its influence on amyloid structure formation.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Lukasz Plachta, Marzena Mach, Magdalena Kowalska, Pawel Wydro
Summary: Resveratrol, a popular phytoalexin found in grapes and red wine, has beneficial effects on the cardiovascular system, exhibits antiviral, antibacterial, and antifungal properties, and may have therapeutic effects against cancer. This study investigates the interaction of resveratrol with model cell membranes, demonstrating changes in their physicochemical parameters and highlighting the role of cholesterol content in resveratrol incorporation. The findings suggest that the molecular mechanism of action of resveratrol may involve interactions with lipid rafts.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Edurne Rujas, Beatriz Apellaniz, Johana Torralba, David Andreu, Jose M. M. Caaveiro, Shixia Wang, Shan Lu, Jose L. Nieva
Summary: This study investigates the role of fusion peptide and Trp-rich membrane proximal external region in HIV-1 fusion and demonstrates that liposome-based formulations containing FP-MPER hybrid peptides can induce the production of specific neutralizing antibodies in rabbits. The results support the use of liposomes as vaccine carriers and the inclusion of lipid membranes in immunogens to elicit specific humoral responses.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Dailin Li, Dingyuan Shi, Lei Wang
Summary: G protein-gated inwardly rectifying potassium (GIRK) channels play a significant role in regulating cell excitability. This study investigated the ion permeation mechanism in GIRK2 mutants using molecular dynamic simulations and QM/MM methods. The results revealed the importance of a multi-ion distribution for ion conduction.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Max J. den Uijl, Arnold J. M. Driessen
Summary: Membrane protein insertion into and translocation across the bacterial cytoplasmic membrane are essential processes facilitated by the Sec translocon. The phospholipid dependence of membrane protein insertion has remained mostly unknown. This study reveals that the insertion of the mannitol permease MtlA into the membrane depends on the presence of phosphatidylglycerol and is stimulated by phosphatidylethanolamine.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Patrick Allen, Adam C. Smith, Vernon Benedicto, Abbas Abdulhasan, Vasanthy Narayanaswami, Enrico Tapavicza
Summary: We explore the stability, size, and structure of nanodiscs formed by the N-terminal domain of apolipoprotein E3 and a variable number of 1,2-dimyristoyl-sn-glycero-3-phosphocholine molecules. Our simulations suggest that nanodiscs containing 240 to 420 DMPC molecules are stable. The antiparallel configuration shows more protein-protein interactions and ionic contacts, as well as greater stability and rigidity compared to the parallel configuration.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Patrick M. Keating, Nicholas P. Schifano, Xinrui Wei, Matthew Y. Kong, Jinwoo Lee
Summary: Lassa virus (LASV) infection is dependent on the fusion of its viral membrane with the host cell membrane, and our study reveals that this fusion process involves pH-dependent conformational changes in the transmembrane domain of LASV. These findings provide valuable insights into the fusion mechanism of LASV and can be utilized in the design of therapeutics to combat Lassa virus infections and prevent its potential spread.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Ashley L. Bennett, Kristen N. Cranford, Austin L. Bates, Christopher R. Sabatini, Hee-Seung Lee
Summary: This study employed molecular dynamics simulations to elucidate the binding, folding, and insertion details of TP10W in the cell membrane. The simulations revealed that TP10W can translocate across the lipid membrane as a monomer, and the charged amino acid side chains can move between lipid leaflets. Comparison with point mutated variants demonstrated significant conformational changes due to charge distribution.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Article
Biochemistry & Molecular Biology
Jessica H. van Wonderen, Jason C. Crack, Marcus J. Edwards, Thomas A. Clarke, Gerhard Saalbach, Carlo Martins, Julea N. Butt
Summary: Electrogenic bacteria transfer excess respiratory electrons to metal oxide particles and electrodes through the MtrCAB complex. The crystal structure of MtrCAB from S. baltica OS185 was resolved, and liquid chromatography mass spectrometry was used to determine the mass values of the three proteins in purified MtrCAB complexes.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
Review
Biochemistry & Molecular Biology
Yi-Ming Chen, Ching-Tai Lu, Chia-Wen Wang, Wolfgang B. Fischer
Summary: A series of dye ligands were ranked based on docking experiments, selecting the most suitable ligands for binding with different proteins. Additionally, a comparison study was conducted on a series of repurposing drugs and known antivirals.
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES
(2024)
