Tuning knot abundance in semiflexible chains with crowders of different sizes: a Monte Carlo study of DNA chains

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We investigate the failure mechanism of stopper knots, with a particular focus on the figure -8 knot as a representative example. Stopper knots are widely used in climbing, sailing, racket stringing, and sewing to maintain tension in ropes, strings, or thr ...

In this thesis, we study the mechanics of tight physical knots. Knots are omnipresent in surgery, climbing, and sailing, with disastrous consequences when the filament or the rope fails to perform its function. Even if the importance of mechanical analysis ...

Knots are the weakest link in surgical sutures, serving as mechanical ligatures between filaments. Exceeding their safe operational limits can cause fatal complications. The empirical nature of present guidelines calls for a predictive understanding of the ...

We present an algorithmic approach to discover, study, and design multistable elastic knots. Elastic knots are physical realizations of closed curves embedded in 3-space. When endowed with the material thickness and bending resistance of a physical wire, t ...

The COVID-19 pandemic has highlighted the necessity to develop fast, highly sensitive and selective virus detection methods. Surface-based DNA-biosensors are interesting candidates for this purpose. Functionalization of solid substrates with DNA must be pr ...

PremiseA novel protocol for rapid plant DNA extraction using microneedles is proposed, which supports botanic surveys, taxonomy, and systematics. This protocol can be conducted in the field with limited laboratory skills and equipment. The protocol is vali ...

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

We perform a combined experimental and computational investigation of the clove hitch knot. We develop a physical model for the clove hitch by tying an elastic rod onto a rigid cylinder. In the experiments, we characterize the mechanical performance, geome ...

Next-generation sequencing (NGS) is an essential technology for DNA identification in genomic research. DNA fragmentation is a critical step for NGS and doing this on-chip is of great interest for future integrated genomic solutions. Here we demonstrate fa ...

We perform a compare-and-contrast investigation between the equilibrium shapes of physical and ideal trefoil knots, both in closed and open configurations. Ideal knots are purely geometric abstractions for the tightest configuration tied in a perfectly fle ...

Nucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N-6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show ...

The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational ch ...

We present a methodology to simulate the mechanics of knots in elastic rods using geometrically nonlinear, full three-dimensional (3D) finite element analysis. We focus on the mechanical behavior of knots in tight configurations, for which the full 3D defo ...

The redox properties of two large DNA fragments composed of 39 base pairs, differing only by an 8-oxoguanine (8oxoG) defect replacing a guanine (G), were investigated in physiological conditions using mixed quantum mechanical/molecular mechanical (QM/MM) m ...

DNA-protein interactions lie at the crux of life's essential processes. As such, various technologies have been developed to characterize these interactions. The distinct advantages of these technologies can be leveraged to study different facets of these ...

Damage to DNA is a central mechanism to the initiation of carcinogenesis. As a consequence, precise DNA damage detection is essential for an effective risk assessment of xenobiotics and constitutes a powerful tool for human biomonitoring and early stage ca ...

Knots are interesting objects to experiment since their topological properties are combined with mechanical properties, fluid mechanics or dynamical properties like unknotting under the excitation of the thermal energy. Knots play also a role in biology be ...

A variety of DNA-binding proteins organizes the chromosomal DNA and regulates gene transcription, and DNA replication and recombination. In particular, for gene regulation there is a category of DNA-binding proteins, the transcription factors, which can de ...

Natural competence for transformation is a primary mode of horizontal gene transfer. Competent bacteria are able to absorb free DNA from their surroundings and exchange this DNA against pieces of their own genome when sufficiently homologous. However, the ...

The specific interaction between DNA and proteins constitutes one of the crucial elements in the regulation of gene expression. This thesis focuses on the development and optimization of two microfluidic-based technologies called SMiLE-seq and FloChIP that ...

Tuning knot abundance in semiflexible chains with crowders of different sizes: a Monte Carlo study of DNA chains

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Capsizing due to friction-induced twist in the failure of stopper knots

Mechanics of Physical Knots: From Filaments in Contact to Surgical Suturing

The strength of surgical knots involves a critical interplay between friction and elastoplasticity

Computational Exploration of Multistable Elastic Knots

Achieving high hybridization density at DNA biosensor surfaces using branched spacer and click chemistry

A field-capable rapid plant DNA extraction protocol using microneedle patches for botanical surveying and monitoring

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Exploring the inner workings of the clove hitch knot

Polydimethylsiloxane microstructure-induced acoustic streaming for enhanced ultrasonic DNA fragmentation on a microfluidic chip

The shapes of physical trefoil knots

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

Finite Element Modeling of Tight Elastic Knots

Redox Properties of Native and Damaged DNA from Mixed Quantum Mechanical/Molecular Mechanics Molecular Dynamics Simulations

Establishing a Ternary System for Optical Monitoring of DNA-Protein Interactions with Single-Walled Carbon Nanotubes

Innovative Techniques and Strategies for a Reliable High-Throughput Genotoxicity Assessment

Experimenting with knots

Exploring on Protein-DNA interactions

Neighbor predation linked to natural competence fosters the transfer of large genomic regions in Vibrio cholerae

Integrated microfluidic tools for the characterization of protein/DNA interactions in vitro and in vivo