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The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…

Biomolecules · Quantitative Biology 2009-11-10 E. Allahyarov , G. Gompper , H. Löwen

The efficient recognition of pathogens by the adaptive immune system relies on the diversity of receptors displayed at the surface of immune cells. T-cell receptor diversity results from an initial random DNA editing process, called VDJ…

Populations and Evolution · Quantitative Biology 2015-04-28 Yuval Elhanati , Anand Murugan , Curtis G. Callan , Thierry Mora , Aleksandra M. Walczak

Twisted van der Waals multilayers are widely regarded as a rich platform to access novel electronic phases, thanks to the multiple degrees of freedom such as layer thickness and twist angle that allow control of their electronic and…

Colloids coated with single-stranded DNA (ssDNA) can bind selectively to other colloids coated with complementary ssDNA. The fact that DNA-coated colloids (DNACCs) can bind to specific partners opens the prospect of making colloidal…

Soft Condensed Matter · Physics 2014-09-24 Stefano Angioletti-Uberti , Patrick Varilly , Bortolo M. Mognetti , Daan Frenkel

Living cells are capable of interacting with their environments in a variety of ways, including cell signalling, adhesion, and directed motion. These behaviours are often mediated by receptor molecules embedded in the cell membrane, which…

Biological Physics · Physics 2023-10-17 Hannah Sleath , Bortolo Mognetti , Yuval Elani , Lorenzo Di Michele

Particles trapped in the evanescent field of an ultrathin optical fibre inter-act over very long distances via multiple scattering of the fibre-guided fields. In ultrathin fibres that support higher order modes, these interac-tions are…

The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat…

Biological Physics · Physics 2025-01-24 Mohammadamin Safdari , Siyu Li , Sanaz Panahandeh , Paul van der Schoot , Roya Zandi

Advances in methods of biological data collection are driving the rapid growth of comprehensive datasets across clinical and research settings. These datasets provide the opportunity to monitor biological systems in greater depth and at…

Molecular Networks · Quantitative Biology 2025-01-20 Joshua Pickard , Cooper Stansbury , Amit Surana , Lindsey Muir , Anthony Bloch , Indika Rajapakse

The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…

Robotics · Computer Science 2016-07-27 Rasmus Fonseca , Dominik Budday , Henry van den Bedem

Surface nanobubbles are nanoscopic spherical-cap shaped gaseous domains on immersed substrates which are stable, even for days. After the stability of a {\it single} surface nanobubble has been theoretically explained, i.e. contact line…

Fluid Dynamics · Physics 2020-02-06 Xiaojue Zhu , Roberto Verzicco , Xuehua Zhang , Detlef Lohse

Recent evidence highlights the usefulness of DNA methylation (DNAm) biomarkers as surrogates for exposure to risk factors for non-communicable diseases in epidemiological studies and randomized trials. DNAm variability has been demonstrated…

Applications · Statistics 2023-02-28 Andrea Cappozzo , Francesca Ieva , Giovanni Fiorito

Living systems are built of multiscale-composites: materials formed of components with different properties that are assembled in complex micro- and nano-structures. Such biological multiscale-composites often show outstanding physical…

Applied Physics · Physics 2022-10-25 Jonas O. Wolff , Daniele Liprandi , Federico Bosia , Anna-Christin Joel , Nicola M. Pugno

Arrays of optically trapped nanoparticles have emerged as a promising platform for the study of complex non-equilibrium phenomena. Analogous to atomic many-body systems, one of the crucial ingredients is the ability to precisely control the…

Naturally occurring networks exhibit quantitative features revealing underlying growth mechanisms. Numerous network mechanisms have recently been proposed to reproduce specific properties such as degree distributions or clustering…

Quantitative Methods · Quantitative Biology 2009-11-10 Manuel Middendorf , Etay Ziv , Chris Wiggins

Polymer composites are ideal candidates for next generation biomimetic soft materials because of their exquisite bottom-up designability. However, the richness of behaviours comes at a price: the need for precise and extensive…

Soft Condensed Matter · Physics 2019-07-30 Davide Michieletto , Robert Fitzpatrick , Rae M Robertson-Anderson

Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…

Soft Condensed Matter · Physics 2020-01-29 Cayke Felipe , Jaeoh Shin , Yulia Loginova , Anatoly B. Kolomeisky

The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…

Biological Physics · Physics 2018-10-04 Jihoon Shin , Junghoon Kim , Sung Ha Park , Tai Hwan Ha

Electrochemical Biosensors are uniquely positioned to offer real-time in vivo molecular sensing due to their robustness to both biofluids and contaminants found in biofluids, and their adaptability for the detection of different analytes by…

Biological Physics · Physics 2024-10-04 Philip S Lukeman

DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of…

Biological Physics · Physics 2019-06-26 Thibaut Lepage , Ivan Junier

Selective control of light is essential for optical science and technology with numerous applications. Nanophotonic waveguides and integrated couplers have been developed to achieve selective coupling and spatial control of an optical beam…