Related papers: Force-induced Unbinding Dynamics in a Multidimensi…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
Wearless dry friction of an elastic block of weight N, driven by an external force F over a rigid substrate, is investigated. The slider and substrate surfaces are both microscopically rough, interacting via a repulsive potential that…
The stability of a $\beta$-sheeted conformation and its transition into a random coil are studied with a 2D lattice biopolymer model. At low temperature and low external force, the polymer folds back and forth on itself and forms a…
The dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally-occurring polymers can navigate a vast phase space and rapidly find their lowest free energy (folded) state. Thus,…
Moire patterns result from setting a 2D material such as graphene on another 2D material with a small twist angle or from the lattice mismatch of 2D heterostructures. We present a continuum model for the elastic energy of these bilayer…
Single-molecule force spectroscopy experiments, as well as a number of other physical systems, are governed by thermally activated transitions out of a metastable state under the action of a steadily increasing external force. The main…
We consider the overdamped dynamics of a paradigmatic long-range system of particles residing on the sites of a one-dimensional lattice, in the presence of thermal noise. The internal degree of freedom of each particle is a periodic…
Cooperative binding affects many processes in biology, but it is commonly addressed only in equilibrium. In this work we explore dynamical cooperativity in driven systems, where the cooperation occurs because some of the bonds change the…
Macro properties of cold atomic gases are driven by few-body correlations, even if the gas has thousands of particles. Quantum systems composed of two and three particles with attractive zero\=/range pairwise interactions are considered for…
The escape process from the native valley for proteins subjected to a constant stretching force is examined using a model for a Beta-barrel. For a wide range of forces, the unfolding dynamics can be treated as one-dimensional diffusion,…
The problem of partially hinged and partially free rectangular plate that aims to represent a suspension bridge subject to some external forces (for example the wind) is considered in order to model and simulate the unstable end behavior.…
We discuss a reaction-diffusion model in one dimension subjected to an external driving force. Each lattice site may be occupied by at most one particle. The particles hop with asymmetric rates (the sum of which is one) to the right or left…
Epithelization, the process whereby an epithelium covers a cell-free surface, is not only central to wound healing but also pivotal in embryonic morphogenesis, regeneration, and cancer. In the context of wound healing, the epithelization…
Multivalent cargo that can interact with substrates via multiple interaction sites exhibit shared characteristics despite being found in different systems at different length-scales. Here, a general analytical model has been developed that…
A dynamical model is proposed to describe the coupled decomposition and profile evolution of a free surface film of a binary mixture. An example is a thin film of a polymer blend on a solid substrate undergoing simultaneous phase separation…
A quantitative model of the mobility of functionalized particles at the interface is pivotal to understanding important systems in biology and nanotechnology. In this work, we investigate the emerging dynamics of particles anchored through…
A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
Dynamic fracture experiments were performed in PMMA over a wide range of velocities and reveal that the fracture energy exhibits an abrupt 3-folds increase from its value at crack initiation at a well-defined critical velocity, below the…
We use recent theoretical advances to develop a new functional form for interatomic forces in bulk silicon. The theoretical results underlying the model include a novel analysis of elastic properties for the diamond and graphitic structures…