Related papers: Probabilistic Model to Treat Flexibility in Molecu…
An improved linear model is developed for elasto-plastic and adhesive contact. New correlations are proposed and validated to estimate the key input parameters of the model, including contact stiffness, yield point, maximum pull-off force…
Spin-glass systems are universal models for representing many-body phenomena in statistical physics and computer science. High quality solutions of NP-hard combinatorial optimization problems can be encoded into low energy states of…
Context. Three-dimensional (3D) reconnection is an important mechanism for efficiently releasing energy during astrophysical eruptive events, which is difficult to be quantitatively analyzed especially within turbulent plasmas. Aims. In…
Normal mode analysis offers an efficient way of modeling the conformational flexibility of protein structures. Simple models defined by contact topology, known as elastic network models, have been used to model a variety of systems, but the…
For the contact of two finite portions of interacting rigid crystalline surfaces, we compute the dependence of the pinning energy barrier on the misfit angle and contact area. The resulting data are used to investigate the distribution of…
Empirical contact networks or interaction networks demonstrate peculiar characteristics stemming from the fundamental social, psychological, physical mechanisms governing human interactions. Although these mechanisms are complex, we test…
Problems of flexible mechanical metamaterials, and highly deformable porous solids in general, are rich and complex due to nonlinear mechanics and nontrivial geometrical effects. While numeric approaches are successful, analytic tools and…
Wrinkling is the phenomenon of out-of-plane deformation patterns in thin walled structures, as a result of a local compressive (internal) loads in combination with a large membrane stiffness and a small but non-zero bending stiffness.…
The respective roles of local and nonlocal interactions in the thermodynamic cooperativity of proteins are investigated using continuum (off-lattice) native-centric G\=o-like models with a coarse-grained C$_\alpha$ chain representation. We…
We present a new ab initio method for calculating effective onsite Coulomb interactions of itinerant and strongly correlated electron systems. The method is based on constrained local density functional theory formulated in terms of…
The plasticity of amorphous solids undergoing shear is characterized by quasi-localized rearrangements of particles. While many models of plasticity exist, the precise relationship between plastic dynamics and the structure of a particle's…
The motion involved in barrier crossing for protein folding are investigated in terms of the chain dynamics of the polymer backbone, completing the microscopic description of protein folding presented in the previous paper. Local reaction…
Understanding interactions between membranes requires measurements on well-controlled systems close to natural conditions, in which fluctuations play an important role. We have determined, by grazing incidence X-ray scattering, the…
We study the influence of the softness of the interparticle interactions on the fragility of a glass former, by considering three model binary mixture glass formers. The interaction potential between particles is a modified Lennard-Jones…
It has recently been suggested that many contact mechanics problems between solids can be accurately studied by mapping the problem on an effective one dimensional (1D) elastic foundation model. Using this 1D mapping we calculate the…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Information delivery using chemical molecules is an integral part of biology at multiple distance scales and has attracted recent interest in bioengineering and communication. The collective signal strength at the receiver (i.e., the…
We present a continuum model trained on molecular dynamics (MD) simulations for cellular membranes composed of an arbitrary number of lipid types. The model is constructed within the formalism of dynamic density functional theory and can be…
A method has been found to analyze Edwards' granular contact force probability functional for a special case. As a result, the granular contact force probability density functions are obtained from first principles for this case. The…
We present the development of the idea to use dynamics in the space of contact maps as a computational approach to the protein folding problem. We first introduce two important technical ingredients, the reconstruction of a three…