Related papers: Quantifying biomolecular diffusion with a "spheric…
We give a description of cell diffusion in a soft tissue, paying special attention to the coupling of force, matter, and microforce balance laws through a suitable dissipation principle. To this end, we cast our framework into a multi-level…
This chapter will provide an overview of how characterizing free-energy landscapes can provide insights into the biophysical properties of DNA, as well as into the behaviour of the DNA assemblies used in the field of DNA nanotechnology. The…
The thermodynamic and kinetic anomalies of supercooled liquids are analyzed from the perspective of energy landscapes. A mean field model, a generalized random energy model of liquids is developed, which exhibits a dynamical transition of…
Subdiffusion is a hallmark of complex systems, ranging from protein folding to transport in viscoelastic media. However, despite its pervasiveness, the mechanistic origins of subdiffusion remain contested. Here, we analyze both Markovian…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
In this paper we present a network model to study the impact of spatial distribution of constituents, coupling between them and diffusive processes in the context of biological situations. The model is in terms of network of mobile elements…
Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
We study segregation and stratification of mixtures of grains differing in size, shape and material properties poured in two-dimensional silos using a microscopic lattice model for surface flows of grains. The model incorporates the…
Spherical multi-layered structures are prevalent in numerous biological systems and engineered applications, including tumor spheroids, layered tissues, and multi-shell nanoparticles for targeted drug delivery. Despite their widespread…
We use a one-dimensional random walk on $D$-dimensional hyper-spheres to determine the critical behavior of statistical systems in hyper-spherical geometries. First, we demonstrate the properties of such a walk by studying the phase diagram…
We use mesoscale simulations to gain insight into the digestion of biopolymers by studying the break-up dynamics of polymer aggregates (boluses) bound by physical cross-links. We investigate aggregate evolution, establishing that the…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
Mechanical single molecule experiments probe the energy profile of biomolecules. We show that in the case of a profile with two minima (like folded/unfolded) periodic driving leads to a stochastic resonance-like phenomenon. We demonstrate…
Most single-molecule studies derive the kinetic rates of native, intermediate, and unfolded states from equilibrium hopping experiments. Here, we apply Kramers kinetic diffusive model to derive the force-dependent kinetic rates of…
Molecular-scale interactions between solvated macromolecules and solid surfaces govern a large number of processes, from biology to engineering. Yet, despite extensive characterization at the macroscopic level, our molecular understanding…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
Growth patterns generated by filamentous organisms (e.g. actinomycetes and fungi) involve spatial and temporal dynamics at different length scales. Several mathematical models have been proposed in the last thirty years to address these…
It has been suggested that major transitions in evolution require the emergence of novelties, often associated to the cooperative behaviour of previously existing objects or agents. A key innovation involves the first cooperative…