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The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
The nanomechanical response of a folded single protein, the natural nanomachine responsible for myriad biological processes, provides insight into its function. The conformational flexibility of a folded state, characterized by its…
Proteins are composed of chains of amino acids that fold into complex three-dimensional structures. Several key features, such as the radius of gyration, fraction of core amino acids $f_{\rm core}$, packing fraction $\langle \phi\rangle$ of…
Recent experiments demonstrated that knots in single DNA strands can be formed by hydrodynamic compression in a nanochannel. In this letter, we further elucidate the underlying molecular mechanisms by carrying out a compression experiment…
The amount and type of self-entanglement of DNA filaments is significantly affected by spatial confinement, which is ubiquitous in biological systems. Motivated by recent advancements in single DNA molecule experiments based on nanofluidic…
Recent progress has been made in the understanding of the physical properties of chromatin -- the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of…
The first level of folding of DNA in eukaryotes is provided by the so called '10 nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging bead on a string…
Cells often divide under mechanical confinement, where surrounding structures restrict shape changes during cytokinesis. Although forces generated during confined division have been measured experimentally, it remains unclear how…
AlphaFold, a groundbreaking protein prediction model, has revolutionized protein structure prediction, populating the AlphaFold Protein Database (AFDB) with millions of predicted structures. However, AlphaFold's accuracy in predicting…
Knotted molecules occur naturally and are designed by scientists to gain special biological and material properties. Understanding and utilizing knotting require efficient methods to recognize and generate knotted structures, which are…
Fibrinogen is a protein found in blood that forms Fibrin polymer network to build a clot during wound healing process when there is a cut in the blood vessel. The fibrin fiber is highly stretchable and shows a complex mechanical properties.…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Understanding the process of protein unfolding plays a crucial role in various applications such as design of folding-based protein engines. Using the well-established kinetostatic compliance (KCM)-based method for modeling of protein…
We propose a combined experimental (Atomic Force Microscopy) and theoretical study of the structural and dynamical properties of nucleosomes. In contrast to biochemical approaches, this method allows to determine simultaneously the DNA…
A new type of knot energy is presented via real life experiments involving a thin resilient metallic tube. Knotted in different ways, the device mechanically acquires a uniquely determined (up to isometry) normal form at least when the…
Force spectroscopy using magnetic tweezers (MT) is a powerful method to probe the physical characteristics of single polymers. Typically, molecules are functionalized for specific attachment to a glass surface at one end and a micron-scale…
We present a theoretical study of the measurements of photoinduced force microscopy (PiFM) for composite molecular systems. Using the discrete dipole approximation, we calculate the self-consistent response electric field of the entire…
Nucleosomes form the basic unit of compaction within eukaryotic genomes and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a…