Article
Physics, Fluids & Plasmas
Xiang Yang, Sahin Buyukdagli, Alberto Scacchi, Maria Sammalkorpi, Tapio Ala-Nissila
Summary: EP mobility reversal refers to the phenomenon where the direction of polymer drift driven by an external electric field is reversed due to the change in sign of the counterion-dressed surface charge. In order to understand this counterintuitive effect, a strong-coupling-dressed Poisson-Boltzmann approach is applied to the cylindrical geometry of the polyelectrolyte-salt system. The derived analytical polymer mobility formula predicts that the increment of monovalent salt, the decrease of multivalent counterion valency, and the increase of the dielectric permittivity of the solvent suppress charge correlations and increase the concentration of multivalent bulk counterions required for EP mobility reversal. Coarse-grained molecular dynamics simulations support these predictions and show the induction of mobility inversion by multivalent counterions at dilute concentrations.
Article
Chemistry, Multidisciplinary
Mathias B. Danielsen, Niels Johan Christensen, Per T. Jorgensen, Knud J. Jensen, Jesper Wengel, Chenguang Lou
Summary: Cationic moieties attached to oligonucleotides increased binding affinity and stability, with the 2'-amino-LNA analogue carrying a triaminated linker showing the most pronounced effect. Molecular modeling revealed salt-bridge formation between positively charged polyamine moieties and the dsDNA targets, resulting in the observed triplex stabilization. All investigated monomers showed increased resistance against 3'-nucleolytic digestion.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Analytical
Youhui Zeng, Ruiying Peng, Yingcai Hu, Pan Luo, Ronghua Yang, Jishan Li, Jing Zheng
Summary: Spherical nucleic acids (SNAs) have been extensively utilized in molecular imaging and tumor therapy due to their adjustable hybridization activity, antinuclease digestion stability, and superior endocytosis. However, the challenge lies in the background signal caused by highly expressed biomarkers in tumors and the inability to precisely release probes at the chosen region. To address this issue, researchers have proposed an endogenous enzyme-activatable functional SNA (Ep-SNA) strategy for spatiotemporally controlled signal amplification molecular imaging and combinational tumor therapy.
ANALYTICAL CHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Judit E. Sponer, Jiri Sponer, Jakub Vyravsky, Roman Matyasek, Ales Kovarik, Wojciech Dudziak, Katarzyna Slepokura
Summary: In this study, it is proposed that guanosine 3',5' cyclic monophosphate could selectively crystallize in an acidic prebiotic pool, which is compatible with subsequent polymerization. The study also suggests that cytidine 3',5' cyclic monophosphate has the ability to selectively accumulate but may not support polymer formation due to its crystal structure.
Article
Chemistry, Multidisciplinary
Tudor Vasiliu, Francesca Mocci, Aatto Laaksonen, Leon De Villiers Engelbrecht, Sergiy Perepelytsya
Summary: This study uses molecular dynamics simulations to investigate the interaction and condensation mechanism between spermidine and DNA. The results show that changes in the accessible space around DNA affect the interaction between DNA and spermidine. This is important for understanding the interaction between DNA and its counterions in compacted environments such as the cellular nucleus.
FRONTIERS IN CHEMISTRY
(2022)
Article
Nanoscience & Nanotechnology
Xin Tang, Wei Li, Liqiu Wang
Summary: A study reveals that droplets on piezoelectric crystal planes can self-propel in various directed motions without the need for chemical inhomogeneity or topological anisotropy. This effect is attributed to anisotropic crystalline structures and has broad applications in different fields.
NATURE NANOTECHNOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Aigui Zhang, Dasharath Kondhare, Peter Leonard, Frank Seela
Summary: The study explores the molecular recognition of complementary purine and pyrimidine bases in the Watson-Crick coding system. Experimental results show that the introduction of specifically modified base pairs can alter the stability and global helical structure of double-stranded DNA. Introducing purine-purine base pairs can lead to novel molecular recognition patterns.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Chemistry, Organic
Rintaro Iwata Hara, Takeshi Wada
Summary: Sequence-dependent off-target effects are a significant concern for antisense oligonucleotide-based drugs, with some side effects induced by RNase H-mediated cleavage of non-target RNAs. However, the use of the artificial cationic oligosaccharide ODAGal4 has been shown to improve single-base discrimination for RNase H cleavage.
ORGANIC & BIOMOLECULAR CHEMISTRY
(2021)
Article
Chemistry, Multidisciplinary
Samantha A. Kennelly, Ramkumar Moorthy, Ruben Silva Otero, Daniel A. Harki
Summary: In this study, four candidate CRDD monomers that mimic endogenous pyrimidines were synthesized and evaluated. It was found that two of them (2-NI and 2-NP) can function as CRDDs, while the other two (3-NP and 2-NB) undergo decomposition or transformation to higher-ordered structures upon photolysis. Additionally, it was discovered that all four pyrimidine mimics exhibit greater stability when base-paired against a previously reported 7-nitroindole CRDD monomer.
CHEMISTRY-A EUROPEAN JOURNAL
(2022)
Review
Chemistry, Multidisciplinary
Congcong Li, Shasha Luo, Jue Wang, Zhifa Shen, Zai-Sheng Wu
Summary: Nucleic acid probes have great potential in biocompatibility and versatility, but their low biostability hinders their in vivo application. In recent years, genetically stable nanostructures offer promising alternatives in biomedical applications.
Article
Multidisciplinary Sciences
Chen Zhang, Fujia Tian, Ying Lu, Bing Yuan, Zhi-Jie Tan, Xing-Hua Zhang, Liang Dai
Summary: DNA deformations can occur upon environmental changes, and an increase in salt concentration leads to DNA overwinding. Our magnetic tweezers experiments and simulations demonstrate that the twist change induced by salt can be quantitatively explained by the screening of electrostatic repulsion and the coupling between twist and DNA diameter. We determine the coupling constant and predict the temperature dependence of DNA twist, finding that the twist-diameter coupling is a common driving force for salt- and temperature-induced DNA twist changes.
Article
Chemistry, Physical
Adwait Datar, Bohdan Tanyhin, Simone Melchionna, Maria Fyta
Summary: This study focuses on controlling the translocation dynamics of polyelectrolytes through coated nanopores for efficient detection. By modeling and analyzing the interactions between the pore, polymer, and detection modality, it provides insights into optimizing the translocation speed and dynamics.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Biochemical Research Methods
Pengcheng Gao, Dagui Wang, Cheng Che, Qun Ma, Xiaoqing Wu, Yajie Chen, Hongquan Xu, Xinchun Li, Yu Lin, Defang Ding, Xiaoding Lou, Fan Xia
Summary: This research introduces a protocol that enhances the sensitivity and specificity of bioanalysis in complex matrices by explicitly dividing the functional elements of solid-state nanochannels.
Article
Chemistry, Multidisciplinary
Mariam Bayoumi, Stefanos K. Nomidis, Kherim Willems, Enrico Carlon, Giovanni Maglia
Summary: The synthetic nanoscale piston presented in the study uses chemical energy to transport molecules against applied bias, allowing for selected DNA molecules to be transported across a nanopore through hybridization and strand displacement reactions. The device demonstrates multiple automated and reciprocating cycles without the need for external bias force, exhibiting characteristics of biological transporters.
Article
Cell Biology
Dorota Rybaczek, Marcelina W. Musialek, Jan Vrana, Beata Petrovska, Ewa G. Pikus, Jaroslav Dolezel
Summary: The article delves into the dynamics of regeneration in Vicia faba from the effects of replication inhibition and cell cycle checkpoint overriding, focusing on DNA damage repair and changes in replication dynamics. It was found that cells induced with PCC exhibit unique replication factor behavior at the start of the regeneration process. Mathematical profiling revealed that even chaotic events are managed with a proper degree of order.
Article
Biochemistry & Molecular Biology
Vladimir Reinharz, Tsvi Tlusty
Editorial Material
Multidisciplinary Sciences
Huan Wang, Myeonggon Park, Ruoyu Dong, Junyoung Kim, Yoon-Kyoung Cho, Tsvi Tlusty, Steve Granick
Summary: In a study conducted by Gunther et al., the control experiment using randomized magnetic field gradient sequences did not align with the findings reported using linear gradients. However, the researchers demonstrate that measurements in their laboratory are consistent using both methods.
Article
Biochemistry & Molecular Biology
Jean-Pierre Eckmann, Tsvi Tlusty
Summary: The advancement of measurement techniques allows for a detailed exploration of living systems, with the need for dimensional reduction to understand high-dimensional data. Living systems achieve dimensional reduction by learning relevant aspects of smooth physical reality, and geometric insights from mathematicians help identify the distinct features of life.
Article
Biophysics
Somya Mani, Tsvi Tlusty
Summary: The rapid advancement of experimental techniques has provided a deeper understanding of complex developmental processes, but little is known about the evolution of complexity in multicellular organisms. Despite the challenge of describing the intricate network of spatiotemporal processes in development, cell type lineage maps can offer insight into developmental trajectories and the evolution of developmental programs. Contrary to common belief, tree-like lineage maps are uncommon, and complex multicellular organisms are more likely to have directed acyclic graphs reflecting multiple converging developmental routes to the same cell type. Additionally, the topology of lineage maps is correlated with the functional property of an organism's ability to regenerate, showing that natural selection prunes low-functioning developmental programs.
BIOPHYSICAL JOURNAL
(2021)
Article
Biology
Somya Mani, Tsvi Tlusty
Summary: This study uses a generative model to test how asymmetric cell division, signaling, and gene regulation can be combined to generate multiple differentiation paths, finding that cell type lineage graphs are unlikely to be tree-like but rather directed acyclic graphs. The majority of model-generated organisms appear to have the ability to regenerate using pluripotent cells.
Article
Biophysics
John M. McBride, Tsvi Tlusty
Summary: Proteins are translated from the N to the C terminus, with an asymmetry in secondary structure enrichment that may accelerate co-translational folding (CTF), especially through a "slowest-first" scheme. This asymmetry can double the folding rate when folding time matches translation time, with prokaryotes showing a greater correspondence due to their need for faster protein production. Accelerating CTF is found to be a significant evolutionary force encoded in structural asymmetry, which interacts with stability and functionality.
BIOPHYSICAL JOURNAL
(2021)
Article
Multidisciplinary Sciences
William D. Pineros, Tsvi Tlusty
Summary: This study demonstrates that chiral symmetry can be spontaneously broken in complex, random chemical systems by exploiting environmental energy sources, which may be a mechanism for the emergence of homochirality in life. The research findings suggest that chiral symmetry breaking may occur spontaneously and generically by harnessing energy sources from external environmental drives.
NATURE COMMUNICATIONS
(2022)
Article
Physics, Multidisciplinary
Ashwani Kr. Tripathi, Tamoghna Das, Govind Paneru, Hyuk Kyu Pak, Tsvi Tlusty
Summary: This study investigates the effect of active noise on enzymatic catalysis in cells, finding that it can significantly accelerate the turnover rate of enzymes, thus revealing enzymatic catalysis as a collective process. This research has important implications for biochemical networks in both living and artificial systems.
COMMUNICATIONS PHYSICS
(2022)
Article
Biochemistry & Molecular Biology
John M. McBride, Jean-Pierre Eckmann, Tsvi Tlusty
Summary: In this study, a model combining chemistry, mechanics, and genetics is presented to explain how these factors interact in the evolution of protein-ligand interactions. The model demonstrates that precision is the key to achieving molecular discrimination, and harder discrimination tasks require more coaction of structure, forces, and movements. The model also suggests that increasing protein size enables the solution of more complicated tasks and makes proteins more evolvable and robust.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Physics, Multidisciplinary
Imran Saeed, Hyuk Kyu Pak, Tsvi Tlusty
Summary: The concept of quasiparticles helps to explain various quantum phenomena in solids. It has been shown that certain properties of a classical system of hydrodynamically interacting particles can also be described by means of quasiparticles.
Article
Physics, Multidisciplinary
Ashwani Kr. Tripathi, Tsvi Tlusty
Summary: This study proposes a simple method to detect the physical features of nanoswimmers by observing their effect on the motion of larger particles. By modeling the swimmers as hydrodynamic force dipoles, the study establishes direct and easy-to-calibrate relations between the observable power spectrum and diffusivity of the tracers, and the dynamic characteristics of the swimmers.
PHYSICAL REVIEW LETTERS
(2022)
Article
Chemistry, Physical
Govind Paneru, Tsvi Tlusty, Hyuk Kyu Pak
Summary: We experimentally observed stochastic resonance (SR) in a nonGaussian active bath without periodic modulation. A Brownian particle in a nanoscale double-well potential, influenced by nonGaussian correlated noise, exhibited equally-spaced peaks in the residence time distribution at integral multiples of tau(P). The first peak was strongest when the mean residence time (tau)(d) matched the conditions 4 tau(c) asymptotic to tau(P) asymptotic to(tau)(d)/2, indicating a new type of bona fide SR. We found that generic SR under periodic modulation, which degrades in strongly correlated continuous noise, could be recovered by the discrete nonGaussian kicks.
Article
Multidisciplinary Sciences
Yaroslav I. I. Sobolev, Ruoyu Dong, Tsvi Tlusty, Jean-Pierre Eckmann, Steve Granick, Bartosz A. A. Grzybowski
Summary: Mathematicians have studied the rolling paths of various shaped bodies, which can be useful in mixing and robotics. These paths are sinusoid-like, but a more general problem was introduced to find a shape that would trace a given infinite periodic trajectory. An algorithm was developed to design these bodies called 'trajectoids', and their existence has unexpected implications for quantum and classical optics.
Article
Physics, Fluids & Plasmas
Tsvi Tlusty
Summary: Hydrodynamics induces non-Hermitian topological phenomena in ordinary soft matter by splitting Dirac cones into bulk Fermi arcs through the interplay of hydrodynamics and elasticity. An analytical model and simulations explain how the emergent singularities shape spectral bands and give rise to a web of van Hove singularity lines in the density of states. This opens avenues for topology-based technology in a broad class of ordinary soft matter, living and artificial alike.
Article
Physics, Fluids & Plasmas
William D. Pineros, Tsvi Tlusty
Summary: The paper demonstrates how to design complex nonequilibrium steady-state density distributions and flux field flows using the large-deviation behavior of a Brownian particle. The method is validated by replicating analytical results and showing the capacity to yield complex prescribed targets. This approach is considered a first step towards designing more complex NESS where general frameworks are lacking.