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The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
In this thesis a new model for calculating the total energy of atomic and solid systems is presented. The model is used to study the properties of the Si(100) surface and dislocation dynamics in the diamond structure. For the Si(100)…
We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical…
Determining the binding pose of a ligand to a protein, known as molecular docking, is a fundamental task in drug discovery. Generative approaches promise faster, improved, and more diverse pose sampling than physics-based methods, but are…
In the paper a novel stochastic algorithm designed to study of chain-like bodies dynamics is introduced. This algorithm models chain movements induced by the tension propagation and its main idea relies on the sequentialization of each…
Large parallel gains in the development of both computational resources as well as sampling methods have now made it possible to simulate dissociation events in ligand-protein complexes with all--atom resolution. Such encouraging progress,…
Soft materials including elastomers and gels are pervasive in biological systems and technological applications. Whereas it is known that intrinsic fracture energies of soft materials are relatively low, how the intrinsic fracture energy…
Motivated by experiments in which single DNA molecules are stretched and twisted we consider a perturbative approach around very high forces, where we determine the writhe distribution in a simple, analytically tractable model. Our results…
Silk is a semi-dilute solution of randomly coiled associating polypeptide chains that crystallise following the stretch-induced disruption, in the strong extensional flow of extrusion, of the solvation shell around their amino acids. We…
Using molecular simulations and theory, we develop an explicit mapping of the contribution of molecular relaxation modes in glassy thermosets to the shear modulus, where the relaxations were tuned by altering the polarity of side groups.…
Microtubules, the primary components of the chromosome segregation machinery, are stabilized by longitudinal and lateral non-covalent bonds between the tubulin subunits. However, the thermodynamics of these bonds and the microtubule…
The dynamics of many macromolecular machines is characterized by chemically-mediated structural changes that achieve large scale functional deployment through local rearrangements of constitutive protein sub-units. Motivated by recent high…
We report in situ measurements of stress evolution in a silicon thin-film electrode during electrochemical lithiation and delithiation by using the Multi-beam Optical Sensor (MOS) technique. Upon lithiation, due to substrate constraint, the…
We consider mechanically generated molecular braids composed of two molecules where long range interactions between them can be considered to be very weak. We describe a model that takes account of the thermal fluctuations of the braid,…
In light of recent advancements in the constitutive modelling of bidisperse and polydisperse entangled linear polymers, we present a new multi fluid generalization of the classic two fluid approximation for flows of inhomogeneous polymer…
Loops undergoing thermal fluctuations are prevalent in nature. Ring-like or cross-linked polymers, cyclic macromolecules, and protein-mediated DNA loops all belong to this category. Stability of these molecules are generally described in…
We derive a class of two-dimensional shell energies for thin elastic bodies exhibiting small-length scale effects modeled via strain-gradient elasticity. Building on the final author's earlier work on plate models, the kinetic and stored…
Fragmentation can be observed in nature and in everyday life on a wide range of length scales and for all kinds of technical applications. Most studies on dynamic failure focus on the behaviour of bulk systems in one, two and three…
There is growing interest in promoting deformation twinning for plasticity in advanced materials, as highly organized twin boundaries are beneficial to better strength-ductility combination in contrast to disordered grain boundaries.…
Change in the interatomic spacing of a two-atom system under tension and compression has been modelled by the elastic deformation of atoms. The critical elastic strain of atoms before separation or cracking from tension was estimated by the…