Article
Chemistry, Physical
Muhammed F. Erguder, Markus Deserno
Summary: This study reveals systematic errors in measuring the elastic properties of lipid membranes through computer simulation and data analysis, and proposes standards and recommendations to assist in the choice of fluctuation analysis. While observable shifts from large-wavelength limits vanish in principle, for intrinsically local parameters, such as twist modulus or splay-tilt coupling, there is no exact limit, making not all choices easily verifiable.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Physics, Fluids & Plasmas
Piotr Nowakowski, Bernd Henning Stumpf, Ana-Suncana Smith, Anna Maciolek
Summary: We study a lipid bilayer membrane model with two order parameters: chemical composition and spatial configuration. We propose a linear coupling between these parameters and calculate correlation functions and order parameter profiles using an exact solution. We also investigate the formation of domains around inclusions on the membrane and compare different ways to quantify their size. Despite its simplicity, the model exhibits interesting features such as the Fisher-Widom line and two distinct critical regions.
Article
Materials Science, Multidisciplinary
R. Ramirez, P. Tarazona, E. Chacon, C. P. Herrero
Summary: A Monte Carlo study was conducted to investigate the thermodynamic behavior of a crystalline membrane described by the Nelson-Peliti Hamiltonian. The study analyzed the case of vanishing in-plane strain and the presence of tensile biaxial strain, as well as identified the region of thermodynamic stability for the flat membrane. The most significant finding was that the unstrained flat membrane is thermodynamically unstable at any finite temperature and requires a critical biaxial stress to achieve stability.
Article
Materials Science, Multidisciplinary
R. Ramirez, P. Tarazona, E. Chacon, C. P. Herrero
Summary: A Monte Carlo study of a crystalline membrane described by the Nelson-Peliti Hamiltonian is conducted. The study investigates the equilibrium properties and thermodynamic stability of the membrane under different strain conditions. The results show that the unstrained membrane is thermodynamically unstable at any finite temperature and a critical stress is needed to stabilize it.
Article
Physics, Multidisciplinary
Pierre Le Doussal, Leo Radzihovsky
Summary: Two-dimensional crystalline membranes in isotropic embedding space exhibit abnormal elasticity and flat phase relevant to graphene. Their thermal fluctuations were studied without exact rotational invariance in the embedding space, focusing on a critical buckling point with application of in-plane stresses. Detailed analysis revealed a transition in a new universality class, predicted as a second-order transition with modified elasticity exponents by the self-consistent screening method, while RG suggested a weakly first-order transition.
PHYSICAL REVIEW LETTERS
(2021)
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
Chemistry, Multidisciplinary
Jonathan Leliaert, Javier Ortega-Julia, Daniel Ortega
Summary: This paper discusses the impact of interactions on the thermal behavior of magnetic nanoparticles and proposes an equation to address this issue. The study found that in larger fields, the heat dissipation caused by interactions tends to be more uniformly distributed among individual particles, which may have implications for magnetic particle hyperthermia.
Article
Biochemistry & Molecular Biology
Yuane Wang, Xuankang Mou, Yongyun Ji, Fan Pan, Shiben Li
Summary: The interaction between macromolecular chains and phospholipid membranes in aqueous solution was investigated using dissipative particle dynamics simulations. The results showed that the macromolecular chains undergo conformational transitions from a coiled to a rod-like structure in both parallel and vertical pulling cases. The simulations also revealed that the membranes can be damaged and repaired during the dynamic processes. The findings contribute to our understanding of the interaction mechanisms between macromolecules and membranes, and they may have potential applications in biology and medicine.
Article
Engineering, Chemical
Lei Tao, Jinlong He, Tom Arbaugh, Jeffrey R. McCutcheon, Ying Li
Summary: This study uses high-throughput molecular dynamics simulations to build a large dataset of polymer's fractional free volume (FFV) and establish the composition-structure relation through machine learning models. By correlating polymer's sub-structures or physico-chemical indexes to FFV, a novel method for efficiently evaluating polymer's FFV is proposed. The study benchmarks the MD simulation protocol, conducts high-throughput MD simulations on over 6500 homopolymers and 1400 polyamides, and successfully predicts FFVs of over 8 million hypothetical polyimides using a feed-forward neural network model, which are validated by MD simulations. This approach shows promising capability for ML virtual screening in the discovery of polymer membranes with exceptional permeability/selectivity, based on the obtained FFVs and reported gas separation performances.
JOURNAL OF MEMBRANE SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Soroush Ziaei, Babak Rashtbari, Jafar Azamat, Hamid Erfan-Niya
Summary: The study investigated the mechanism of nanotubes penetrating cell membranes, focusing on boron nitride nanotubes and carbon nanotubes. Functional groups and polymers were used to improve the biocompatibility and solubility of the nanotubes. Various analytical techniques were employed to examine the interaction between the nanotubes and drugs in biological media. The findings showed that the tethering of tetra ethylene glycol enhanced the water molecules surrounding the nanotubes and improved the durability of the drugs.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Physics, Multidisciplinary
D. Collomb, S. J. Bending, A. E. Koshelev, M. P. Smylie, L. Farrar, J-K Bao, D. Y. Chung, M. G. Kanatzidis, W-K Kwok, U. Welp
Summary: Quantitative magnetic imaging of superconducting vortices in RbEuFe4As4 showed a pronounced suppression of superfluid density near the magnetic ordering temperature, indicating a significant exchange interaction between the superconducting and magnetic subsystems. This has important implications for future investigations of physical phenomena arising from the interplay between them.
PHYSICAL REVIEW LETTERS
(2021)
Article
Materials Science, Multidisciplinary
Jin Yu, Mikhail Katsnelson, Tianzhong Zhang, Shengjun Yuan
Summary: This study explores the distribution of ripples in graphene membranes through simulations and analysis, and finds that the ripple density is inversely correlated with the ratio of ripple height to diameter. It provides specific quantitative information on the ripple distribution in graphene and offers new insights applicable to other 2D materials.
Article
Physics, Applied
Prakiran Baidya, Vivas Bagwe, Pratap Raychaudhuri, Aveek Bid
Summary: A study of charge carrier dynamics in a novel two-dimensional superconducting van der Waals heterostructure reveals a percolative superconducting transition and non-Gaussian components indicative of long-range correlation.
APPLIED PHYSICS LETTERS
(2022)
Article
Food Science & Technology
Carlos E. Zambra, Luis Puente-Diaz, Kong Ah-Hen, Carlos Rosales, Diogenes Hernandez, Roberto Lemus-Mondaca
Summary: It is common to ignore volume changes in numerical simulations of food drying, leading to lower accuracy. This study develops a three-dimensional model that incorporates volume changes and considers the asymmetry of shrinkage. Experimental data on fruit drying kinetics and asymmetric shrinkage mode support the model's effectiveness, reducing the relative error by over 4 times compared to simulations without volume changes. This proposed model proves to be a useful method for more accurate modeling of drying processes.
Article
Multidisciplinary Sciences
Nika Marusic, Lado Otrin, Jonas Rauchhaus, Ziliang Zhao, Fotis L. Kyrilis, Farzad Hamdi, Panagiotis L. Kastritis, Rumiana Dimova, Ivan Ivanov, Kai Sundmacher
Summary: Biomimetic polymer/lipid hybrid compartments have great potential as substitutes for natural liposomes. This study explores the protein-free fusion of these semisynthetic membranes and finds that the membrane mixing of oppositely charged hybrids exceeds that of liposomes. The charge is not the sole determinant of the final adenosine triphosphate synthesis rate, and the fusion strategy can be used for the delivery of membrane proteins and the automation of synthetic cell assembly.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Tine Maja Frimann, Suk Kyu Ko, Pernille Harris, Jens Thostrup Bukrinski, Gunther H. J. Peters
Summary: In this study, we used molecular dynamics simulations to investigate the binding of glucagon-like peptide-1 (GLP-1) and acylated GLP-1 analogues with the endogenous receptor (GLP-1R). The results showed that the fatty acid (FA) chain structure, acylation position on the peptide, and presence of a linker all played important roles in the binding. Analysis of the simulations revealed that the major differences between the systems were due to the FA interactions and positioning of acylation on the peptide. Hydrophobic interactions between the FA chain and a hydrophobic patch on the extracellular domain significantly contributed to the binding affinity. Furthermore, the presence of a charged linker between the peptide and FA chain could stabilize the complex by forming hydrogen bonds. These findings provide important insights into designing acylated agonists for GLP-1R.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Chemistry, Physical
Helena D. D. Tjornelund, Jesper Brask, John M. M. Woodley, Gunther H. J. Peters
Summary: In this study, an optimized protocol for controlling the initial water activity in organic reaction mixtures with soluble lipase was proposed. The protocol ensures reproducible and consistent enzyme activity measurements. The importance of consistent stirring and volume correction to compensate for solvent evaporation was highlighted. The study also tested the protocol on soluble and immobilized lipase and found similar water activity profiles and the highest enzyme activity in hexane. This optimized protocol expands the possibilities for studying enzyme kinetics.
Article
Biochemistry & Molecular Biology
Mikkel Madsen, Andreas Prestel, Eva Madland, Peter Westh, Anne Tondervik, Havard Sletta, Gunther H. J. Peters, Finn L. L. Aachmann, Birthe B. B. Kragelund, Birte Svensson
Summary: In order to improve the control of biomaterial property design, a better understanding of the complex coacervation between anionic polysaccharides and proteins is essential. This study investigated the initial steps of condensate formation between beta-lactoglobulin A (beta-LgA) and various alginate oligosaccharides (AOSs), providing structural details of their multivalent interactions. The results revealed that beta-LgA exhibited high multivalency and showed similar affinities for AOSs with increasing degree of polymerization. NMR analyses identified different binding sites for AOSs on beta-LgA, and molecular docking indicated that the AOSs have similar orientations at the preferred binding site. The study highlights the dynamic nature of the AOS binding and its role in the formation of disordered beta-LgA alginate coacervate structures.
Article
Chemistry, Physical
Jeppe C. Dyre, Ulf R. Pedersen
Summary: In this study, an alternative zero-parameter prediction method based on the isomorph theory and properties at a single reference state point is proposed to accurately predict the melting line of the WCA system at high temperatures, while the hard-sphere theory performs better at lower temperatures. Additionally, the results show that the excellent predictions of the isomorph theory for the WCA potential at higher temperatures may be partly due to a cancellation of errors between the two basic assumptions.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Chemistry, Physical
Trond S. Ingebrigtsen, Jeppe C. Dyre
Summary: The difference in structure and dynamics between size-polydisperse and energy-polydisperse liquids is studied numerically. It is found that while size-polydisperse systems show changes in average structure and dynamics, energy-polydisperse systems do not. Even with extreme energy polydispersity leading to phase separation, the average structure and dynamics remain unchanged. This is consistent with the fact that forces on individual particles do not change with energy polydispersity.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Physical
Zahraa Sheydaafar, Jeppe C. Dyre, Thomas B. Schroder
Summary: Isomorphs are curves in the thermodynamic phase diagram that exhibit structural and dynamic invariance. Tracing isomorphs can be done using different methods, such as configurational-adiabat and direct-isomorph-check. A recent force-based method, which only requires a single equilibrium configuration, shows promising results in atomic systems. In this study, we test the generalization of this method to molecular systems and compare it to simulations of three different molecular models.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Chemistry, Multidisciplinary
Andreas Erichsen, Gunther H. J. Peters, Sophie R. Beeren
Summary: Delta-CD, a minor component of a complex mixture of linear and cyclic glucans, can be synthesized in unprecedented yields by employing a unique template in an enzyme-mediated dynamic combinatorial library of cyclodextrins. NMR spectroscopy studies revealed that delta-CD can form pseudorotaxanes with up to three bolaamphiphiles. This research provides a new method for the preparative-scale synthesis of delta-CD.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2023)
Article
Medicine, Research & Experimental
Alina Kulakova, Dillen Augustijn, Inas El Bialy, Lorenzo Gentiluomo, Maria Laura Greco, Stefan Hervo-Hansen, Sowmya Indrakumar, Sujata Mahapatra, Marcello Martinez Morales, Christin Pohl, Marco Polimeni, Aisling Roche, Hristo L. Svilenov, Andreas Tosstorff, Matja Zalar, Robin Curtis, Jeremy P. Derrick, Wolfgang Friess, Alexander P. Golovanov, Mikael Lund, Allan Norgaard, Tarik A. Khan, Gunther H. J. Peters, Alain Pluen, Dierk Roessner, Werner W. Streicher, Christopher F. van der Walle, Jim Warwicker, Shahid Uddin, Gerhard Winter, Jens Thostrup Bukrinski, Asmund Rinnan, Pernille Harris
Summary: Therapeutic proteins are difficult to develop due to their complexity and the need for an acceptable formulation. A universal formulation strategy is currently lacking. This study used high-throughput characterization to analyze 14 different proteins formulated under various conditions. pH and ionic strength were identified as the most important factors affecting protein stability. Prediction methods were also developed for real-time and accelerated stress stability.
MOLECULAR PHARMACEUTICS
(2023)
Article
Biochemistry & Molecular Biology
Ida M. Vedel, Andreas Prestel, Zhenwei Zhang, Natalia T. Skawinska, Holger Stark, Pernille Harris, Birthe B. Kragelund, Gunther H. J. Peters
Summary: The structure and dynamics of Tryptophan hydroxylase 2 (TPH2) and its regulatory mechanism were investigated using NMR spectroscopy and cryo-EM techniques. The results revealed the complexity of TPH2 regulation and the presence of a monomer-dimer equilibrium. These findings provide important insights for understanding the regulatory mechanism of TPH2.
Article
Physics, Condensed Matter
Daniel Jespersen, Lorenzo Costigliola, Jeppe C. Dyre, Shibu Saw
Summary: This paper investigates the existence of isomorphs in size-polydisperse Lennard-Jones systems described by active Ornstein-Uhlenbeck particle (AOUP) dynamics. Isomorphs, which are curves of invariant structure and dynamics, are traced out from a single steady-state configuration using the configurational-temperature method. The study demonstrates good isomorph invariance for three uniform-distribution polydispersities and compares the results to active-matter isomorphs generated by another method.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2023)
Article
Virology
Karen Anbro Gammeltoft, Yuyong Zhou, Line Abildgaard Ryberg, Long V. Pham, Alekxander Binderup, Carlos Rene Duarte Hernandez, Anna Offersgaard, Ulrik Fahnoe, Gunther Herbert Johannes Peters, Santseharay Ramirez, Jens Bukh, Judith Margarete Gottwein
Summary: The study reveals the risk of drug resistance to Nirmatrelvir, a drug targeting the SARS-CoV-2 main protease. The experiment shows that SARS-CoV-2 selected under treatment with the protease inhibitor Boceprevir exhibits cross-resistance to Nirmatrelvir, with up to 7.3-fold increased effective concentration compared to the original virus. Sequence analysis identifies Mpro substitutions L50F and A173V in the escaped viruses, and A173V is found to be the main driver of resistance. The findings contribute to a comprehensive understanding of the resistance profile of Nirmatrelvir and can inform population monitoring and pandemic preparedness.
Article
Food Science & Technology
Hongkai Zhu, Jingyuan Liu, Mogens L. Andersen, Gunther H. J. Peters, Marianne N. Lund
Summary: The reaction kinetics between methylglyoxal (MGO) and epigallocatechin gallate were studied, and a model was developed to predict the trapping capacity of MGO based on the molecular properties of seven flavonoids. The model was created using synthetic minority oversampling technique and principal component regression (PCR) and back-propagation neural network algorithm. The PCR model based on the first six principle components showed high accuracy, with a root-mean-square error value of 8.02 x 10-7. This work provides quantitative structure-activity models for rapid and accurate prediction of the trapping rate constant of MGO by flavonoids.
Article
Chemistry, Physical
Trond S. Ingebrigtsen, Jeppe C. Dyre
Summary: Size-polydisperse liquids are commonly used as models for studying supercooled liquids and glasses formed by colloidal systems. In this study, we investigated the difference in structure and dynamics between size-polydisperse and energy-polydisperse liquids using numerical simulations. The results showed that the average structure and dynamics remain unchanged even for strong energy polydispersity, while they vary significantly in size-polydisperse systems. The distribution of forces on individual particles is believed to be the key factor contributing to these differences.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Biochemistry & Molecular Biology
Helena D. Tjornelund, Jesper Vind, Jesper Brask, John M. Woodley, Gunther H. J. Peters
Summary: This study investigates the molecular mechanism of the specific activity of Candida antarctica lipase B (CALB) in low-water environments using molecular dynamics simulations. Based on experiments and simulations, four criteria influencing the performance of the enzyme in organic media were proposed and it was shown that specific mutants can resist changes in water activity.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)