Related papers: Quantifying biomolecular diffusion with a "spheric…
The onset of life is often framed around membrane bound compartments and encoded metabolism, leaving unresolved how spatial organization arose before stable boundaries. In this context, environmental gradients are usually treated as…
Much of our understanding of ecological and evolutionary mechanisms derives from analysis of low-dimensional models: with few interacting species, or few axes defining "fitness". It is not always clear to what extent the intuition derived…
A simple lattice model, recently introduced as a generalization of the Wako--Sait\^o model of protein folding, is used to investigate the properties of widely studied molecules under external forces. The equilibrium properties of the model…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
Dynamic properties of molecular motors that fuel their motion by actively interacting with underlying molecular tracks are studied theoretically via discrete-state stochastic ``burnt-bridge'' models. The transport of the particles is viewed…
Understanding how species persist under interacting stressors is a central challenge in ecology. We develop a spatially explicit reaction-diffusion framework to investigate competing species in landscapes shaped by climate variability,…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
Free boundaries of biofilms advancing on surfaces evolve according to conservation laws coupled with systems of partial differential equations for velocities, pressures and chemicals affecting cell behavior. Thin film approximations lead to…
The transport of deformable particles through porous media underlies a wealth of applications ranging from filtration to oil recovery to the transport and spreading of biological agents. Using direct numerical simulations, we analyze the…
We investigate the dynamics of a particle moving randomly along a disordered hetero-polymer subjected to rapid conformational changes which induce superdiffusive motion in chemical coordinates. We study the antagonistic interplay between…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…
Originating from the diffusion phenomenon in physics that describes particle movement, the diffusion generative models inherit the characteristics of stochastic random walk in the data space along the denoising trajectory. However, the…
Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
A protein's function depends critically on its conformational ensemble, a collection of energy weighted structures whose balance depends on temperature and environment. Though recent deep learning (DL) methods have substantially advanced…
Dynamical connectivity graphs, which describe dynamical transition rates between local energy minima of a system, can be displayed against the background of a disconnectivity graph which represents the energy landscape of the system. The…
Two phase solid-fluid mixture models are ubiquitous in biological applications. For instance, models for growth of tissues and biofilms combine time dependent and quasi-stationary boundary value problems set in domains whose boundary moves…
Diffusion is a fundamental phenomenon that occurs ubiquitously in nature and remains the subject of continuous research interest. Understanding diffusion is a key to understanding leaving systems. In this Chapter, I discuss diffusion of…
We discuss multiscale simulations of long biopolymer translocation through wide nanopores that can accommodate multiple polymer strands. The simulations provide clear evidence of folding quantization, namely, the translocation proceeds…
We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta-…