Related papers: Dynamic Response of Adhesion Complexes: Beyond the…
In the Master's thesis of the author, we investigate certain aspects of gravitational physics that emerge from stochastic toy models of holographic gauge theories. We begin by reviewing field theory thermodynamics, black hole thermodynamics…
The unbinding process of a protein-ligand complex of major biological interest was investigated by means of a computational approach at atomistic classical mechanical level. An energy minimisation-based technique was used to determine the…
We present a theory for the reverse analysis on the sequence information of a single H/P two-letter random hetero-polymer (RHP) from its force-extension(f-z) curves during quasi static stretching. Upon stretching of a self-assembled RHP, it…
DNA adsorption and naturation is modeled via two interacting flexible homopolymers coupled to a solid surface. DNA denatures if the entropy gain for unbinding the two strands overcomes the loss of binding energy. When adsorbed to a surface,…
We consider the driven dynamics of a probe particle moving through an assembly of particles with competing long-range repulsive and short-range attractive interactions, which form crystal, stripe, labyrinth, and bubble states as the ratio…
The dissociative adsorption of hydrogen on Pd(100) has been studied by ab initio quantum dynamics and ab initio molecular dynamics calculations. Treating all hydrogen degrees of freedom as dynamical coordinates implies a high dimensionality…
Biological macromolecules have complex and non-trivial energy landscapes, endowing them a unique conformational adaptability and diversity in function. Hence, understanding the processes of elasticity and dissipation at the nanoscale is…
From flocks of birds to biomolecular assemblies, systems in which many individual components independently consume energy to perform mechanical work exhibit a wide array of striking behaviors. Methods to quantify the dynamics of these so…
Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…
We present the Multi-Particle-Collision (MPC) dynamics approach to simulate properties of low-dimensional systems. In particular, we illustrate the method for a simple model: a one-dimensional gas of point particles interacting through…
Molecular self-assembly on surfaces constitutes a powerful method for creating tailor-made surface structures with dedicated functionalities. Varying the intermolecular interactions allows for tuning the resulting molecular structures in a…
The ground states and collective excitations of trapped Fermion gases consisting of atoms with magnetic dipole moment are studied using a time-dependent density-matrix approach. The advantages of the density-matrix approach are that…
We investigate the thermodynamics and kinetics of DNA hairpins that fold/unfold under the action of applied mechanical force. We introduce the concept of the molecular free energy landscape and derive simplified expressions for the force…
We consider the response of a multicomponent body to $n$ fields, such as electric fields, magnetic fields, temperature gradients, concentration gradients, etc., where each component, which is possibly anisotropic, may cross couple the…
Although the stretching of polymers and biomolecules is important in numerous settings, their response when confined to two-dimensions is relatively poorly-studied. In this paper, we derive closed-form analytical expressions for the…
The elastic behavior of materials operating in the linear regime is constrained, by definition, to operations that are linear in the imposed deformation. Though the nonlinear regime holds promise for new functionality, the design in this…
Cells sense the geometry and stiffness of their adhesive environment by active contractility. For strong adhesion to flat substrates, two-dimensional contractile network models can be used to understand how force is distributed throughout…
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…
A key challenge in performing experiments with microparticles is controlling their adhesion to substrates. For example, levitation of a microparticle initially resting on a surface requires overcoming the surface adhesion forces to deliver…
The nature of adhesion of droplets to surfaces is a long pending scientific question. With the evolution of complex surfaces, quantification and prediction of these forces become intricate. Nevertheless, understanding these forces is highly…