Article
Biochemistry & Molecular Biology
Qingwen Bai, Zhijun Liu, Jiaxin Chen, Dehai Liang
Summary: In this study, biphasic coacervate droplets formed by poly(L-lysine) (PLL), quaternized dextran (Q-dextran), and single-stranded oligonucleotides (ss-oligo) were used as a model of membrane-less organelles (MLOs). The results show that Bovine Serine Albumin (BSA) effectively regulates the LLPS process by controlling the phase distribution, morphologies, and kinetics. The study suggests that MLOs could be controlled by the crowded environment, providing further insights into the life processes in cells.
Article
Multidisciplinary Sciences
Hannes Ausserwoeger, Georg Krainer, Timothy J. Welsh, Nels Thorsteinson, Ella de Csillery, Tomas Sneideris, Matthias M. Schneider, Thomas Egebjerg, Gaetano Invernizzi, Therese W. Herling, Nikolai Lorenzen, Tuomas P. J. Knowles
Summary: This study systematically analyzed the impact of surface patch properties on antibody nonspecificity using a designer antibody library and single-stranded DNA. The results showed that the binding affinity between antibodies and single-stranded DNA is driven mainly by a hydrophobic patch in the complementarity-determining regions. It was also found that the nonspecific binding affinity correlates with a trade-off between the hydrophobic and total charged patch areas, and that a change in formulation conditions at low ionic strengths leads to DNA-induced antibody phase separation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Biochemistry & Molecular Biology
Elizaveta E. Alemasova, Olga Lavrik
Summary: This review discusses the formation of biomolecular condensates and the role of site-specific interactions and percolation in cellular condensate formation. Using the example of multivalent poly(ADP-ribose) molecule, the influence of its structural features on condensate formation is examined.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
German Rivas, Allen P. Minton
Summary: This article reviews the various types of nonspecific interactions between proteins and other macromolecules and supramolecular structures in the cellular interior, and summarizes the current state of knowledge and suggestions for future research.
ANNUAL REVIEW OF BIOCHEMISTRY
(2022)
Article
Chemistry, Physical
Milan Kumar Hazra, Yaakov Levy
Summary: In this study, the contribution of cation-π interactions to the stability of biomolecular condensates formed via liquid-liquid phase separation is investigated using coarse-grained molecular dynamics simulations. The results demonstrate that cation-π interactions can significantly enhance the stability of peptide condensates, especially for peptides with higher aromatic residue content or less charge clustering. Moreover, the contribution of cation-π interactions to droplet stability increases with increasing ionic strength. Therefore, designing condensates with desired biophysical characteristics requires understanding and quantification of not only individual interactions but also cross-talks involving charge-charge, π-π, and cation-π interactions.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Mayu Nishizawa, Erik Walinda, Daichi Morimoto, Benjamin Kohn, Ulrich Scheler, Masahiro Shirakawa, Kenji Sugase
Summary: ATP, a well-studied metabolite in living systems, interacts weakly but measurably with various proteins through noncovalent interactions, altering protein hydration and potentially providing temporary protection to protein surfaces. ATP is proposed to be a general nonspecific binder of proteins at physiological concentrations, forming oligomeric states via magnesium-chelating mechanisms. This metabolite-mediated protein surface protection could play a role in cellular processes.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
(2021)
Article
Biochemistry & Molecular Biology
Zachary R. Grese, Alliny C. S. Bastos, Lohany D. Mamede, Rachel L. French, Timothy M. Miller, Yuna M. Ayala
Summary: TDP-43 is an RNA-binding protein that forms ribonucleoprotein condensates through liquid-liquid phase separation, playing a central role in regulating gene expression and protein homeostasis. RNA binding promotes TDP-43 condensation through specific interactions, maintaining the liquid-like properties of condensates. Defects in this RNA-mediated activity may contribute to TDP-43-associated pathogenesis, particularly in neurodegenerative disorders such as ALS and frontotemporal dementia.
Article
Polymer Science
Ya-Chen Chuang, Yu-Chia Chang, Meng-Tzu Tsai, Ting-Wei Yang, Meng-Tse Huang, Shao-Hua Wu, Chi Wang
Summary: The phase diagram of a polymer solution can determine its electrospinnability and transition temperatures. Low-temperature electrospinning can successfully produce uniform nanofibers, while electrospinning within a specific temperature range is feasible, but it becomes problematic at higher temperatures due to the enhanced gel elasticity.
Article
Chemistry, Physical
Yu Zheng, Ali A. Alizadehmojarad, Sergei M. Bachilo, R. Bruce Weisman
Summary: Understanding the conformations of single-stranded DNA on carbon nanotube surfaces is crucial for various applications. In this study, we found evidence of partial desorption of DNA strands from the nanotube surface under common conditions. This desorption is caused by steric interference between neighboring DNA strands and decreases with decreasing concentration of free DNA.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biophysics
Ian Seim, Christine A. Roden, Amy S. Gladfelter
Summary: Viruses efficiently package their genomes through specific packaging signals and liquid-liquid phase separation (LLPS) of viral proteins. The positioning and abundance of LLPS-promoting elements play a critical role in genome compaction and cyclization.
BIOPHYSICAL JOURNAL
(2021)
Article
Physics, Fluids & Plasmas
X. B. Xu, T. Tang, Z. H. Wang, X. N. Xu, G. Y. Fang, M. Gu
Summary: This study investigates the nonequilibrium behaviors of classic particles with competing interactions in a two-dimensional logarithmic trap. The research reveals a surprising dynamics induced by a quench, showing rich dynamic patterns that depend on confinement strength and trap size under circular confinement. Furthermore, the emergence of dynamic structure transformation in collectively diffusive motions coincides with a mode transition from superdiffusion to subdiffusion.
Article
Multidisciplinary Sciences
Vikas A. Tillu, James Rae, Ya Gao, Nicholas Ariotti, Matthias Floetenmeyer, Oleksiy Kovtun, Kerrie-Ann Mcmahon, Natasha Chaudhary, Robert G. Parton, Brett M. Collins
Summary: The study highlights the essential role of the three disordered domains of Cavin1 in caveola formation and dynamic trafficking, as well as the fuzzy electrostatic interactions between Cavin1 and caveolin-1 proteins, combined with membrane lipid interactions, in generating membrane curvature and maintaining a stable caveola coat.
NATURE COMMUNICATIONS
(2021)
Review
Cell Biology
Ying Zhang, Yi Xiang See, Vinay Tergaonkar, Melissa Jane Fullwood
Summary: This review provides an overview of the current knowledge on human silencers, with a focus on the roles of chromatin interactions and phase separation. The review also proposes future directions for research on human silencers.
Article
Multidisciplinary Sciences
Sarah E. Cabral, Jessica P. Otis, Kimberly L. Mowry
Summary: RNA localization and biomolecular condensate formation are important strategies for organizing the cytoplasm and generating cellular polarity. The study reveals that RNA-protein interactions drive the recruitment of PTBP3 and localized RNA to biomolecular condensates. Multivalent interactions regulate the dynamics of PTBP3 after localization. Furthermore, RNA plays a crucial role in maintaining the PTBP3-RNA condensates.
Article
Physics, Multidisciplinary
L. Caprini, H. Loewen
Summary: Within a simple model of attractive active Brownian particles, flocking behavior can be observed even without alignment interactions. The transition from a disordered phase to a flocking phase is characterized by the emergence of a single flocking cluster. The spatial connected correlation function of particle velocities can confirm this scenario and distinguish between flocking and non-flocking configurations. Our predictions can be tested in experiments with various systems showing flocking behavior.
PHYSICAL REVIEW LETTERS
(2023)
Article
Physics, Multidisciplinary
Shaltiel Eloul, Wilson C. K. Poon, Oded Farago, Daan Frenkel
PHYSICAL REVIEW LETTERS
(2020)
Article
Multidisciplinary Sciences
Jorge R. Espinosa, Jerelle A. Joseph, Ignacio Sanchez-Burgos, Adiran Garaizar, Daan Frenkel, Rosana Collepardo-Guevara
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2020)
Article
Chemistry, Physical
Xipeng Wang, Simon Ramirez-Hinestrosa, Daan Frenkel
JOURNAL OF PHYSICAL CHEMISTRY B
(2020)
Article
Chemistry, Physical
S. W. Coles, E. Mangaud, D. Frenkel, B. Rotenberg
Summary: This study presents a method to further reduce the variance of force-based estimators by considering optimal linear combinations, which has been comparatively less explored in molecular simulations. The approach not only effectively reduces the variance, but also corrects a defect of the initial estimators, highlighting the underexplored potential of control variates in estimating observables from molecular simulations.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
H. A. Vinutha, Daan Frenkel
Summary: By utilizing a recently developed technique and different methods to calculate the solubility and chemical potential differences of amorphous solids, it is found that using the Jarzynski method for computing the chemical potential of components yields more accurate results for solubility and chemical potential calculations of glassy materials.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Vikram Khanna, Jamshed Anwar, Daan Frenkel, Michael F. Doherty, Baron Peters
Summary: This paper extends previous work on free energy calculations of crystals using a center of mass constraint and finite-size corrections, focusing on crystals with differing spring constants. By comparing free energies calculated with different spring constants, the theory is tested and the intrinsic finite-size effects are eliminated. The calculations help demonstrate the impact of these finite-size corrections on the absolute free energy of crystals.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
H. A. Vinutha, Daan Frenkel
Summary: The study demonstrates that plausible free-energy estimates of a Kob-Andersen glass can be obtained using the Jarzynski relation, which matches well with the extrapolated value of the supercooled liquid in the glassy regime. This finding is significant for the broader interest in the field of thermodynamic methods.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Physical
Yawei Liu, Jiachen Wei, Daan Frenkel, Asaph Widmer-Cooper
Summary: In this study, a coarse-grained model based on the DPD method was developed to investigate the aggregation of CTAB molecules on gold surfaces. The model can describe the structural changes of CTAB aggregates on gold surfaces and around gold nanorods, predicting the distribution of ligand density within the CTAB layer.
MOLECULAR SIMULATION
(2022)
Review
Physics, Condensed Matter
Simon Ramirez-Hinestrosa, Daan Frenkel
Summary: The paper uses a unified framework to describe diffusio-osmosis and reports non-equilibrium molecular dynamics (NEMD) on such systems. Different simulation methods are explored to highlight technical problems in calculations, with two NEMD methods used for diffusiophoresis.
EUROPEAN PHYSICAL JOURNAL B
(2021)
Article
Chemistry, Physical
Yagyik Goswami, Vishwas V. Vasisht, Daan Frenkel, Pablo G. Debenedetti, Srikanth Sastry
Summary: This study investigated the kinetics of crystallization in deeply supercooled liquid silicon using computer simulations and Stillinger-Weber potential. The research focused on the presence of free energy barriers to crystallization at state points near a liquid-liquid phase transition, providing strong evidence against the possibility of slow, spontaneous crystallization in those states. The results also discussed the effect of changes in the microscopic structure of the metastable liquid on the free energy barrier heights.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Chemistry, Multidisciplinary
Alexander Cumberworth, Daan Frenkel, Aleks Reinhardt
Summary: Nucleation is the rate-determining step in the kinetics of self-assembly processes. The importance of nucleation in DNA-origami self-assembly is unclear. Monte Carlo simulations of a lattice model of DNA origami revealed that some designs have a nucleation barrier, which disappears at lower temperatures. The height of the nucleation barrier depends on the coaxial stacking of adjacent staples, which can be modified with staple design. Creating or eliminating the nucleation barrier may have implications for optimizing assembly times, yields, and developing fast molecular sensors.
Article
Physics, Multidisciplinary
Xipeng Wang, Jure Dobnikar, Daan Frenkel
Summary: In this study, we conducted simulations to test the Onsager reciprocity relations in a nonequilibrium steady state system. Our results demonstrate that these relations still hold true in the linear regime, even when the system is perturbed from a nonequilibrium steady state in a way that does not satisfy time-reversal symmetry. This suggests that the Onsager relations are applicable beyond their original range and may be relevant for transport in driven or active systems.
PHYSICAL REVIEW LETTERS
(2022)
Article
Chemistry, Physical
Shaltiel Eloul, Daan Frenkel
Summary: The study proposes a switchable nano-scale fluid pump, driven by exothermic surface reactions, which could be controlled electro-chemically. Simulations show that the simplicity of the pump design could make it attractive for micro/nano-fluidics applications.
Article
Physics, Fluids & Plasmas
H. A. Vinutha, Daan Frenkel
Article
Chemistry, Physical
Xipeng Wang, Simon Ramirez-Hinestrosa, Jure Dobnikar, Daan Frenkel
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2020)