Related papers: Probabilistic Model to Treat Flexibility in Molecu…
Dynamic rupture propagation along an interface between two different elastic solids under shear dominated loading is studied numerically by a 2-D lattice particle model (LPM). The configuration of the lattice particle model consists of two…
Particle based methods such as the Discrete Element Method and the Lattice Spring Method may be used for describing the behaviour of isotropic linear elastic materials. However, the common bond models employed to describe the interaction…
Predicting three dimensional residue-residue contacts from evolutionary information in protein sequences was attempted already in the early 1990s. However, contact prediction accuracies of methods evaluated in CASP experiments before CASP11…
Throughout developmental biology and ecology, transport can be driven by nonlocal interactions. Examples include cells that migrate based on contact with pseudopodia extended from other cells, and animals that move based on their vision of…
We present contact radius and curvature corrections to the nonlocal contact formulation that take into account multi-particle interactions in elastic confined granular systems. The nonlocal contact formulation removes the classical…
We propose a deterministic particle method for a one-dimensional nonlocal equation with interactions through the repulsive Morse potential. We show that the particle method converges as the number of particles goes to infinity towards weak…
We derive expressions for determination of the stress and the elastic constants in systems composed of particles interacting via non-central two-body potentials as thermal averages of products of first and second partial derivatives of the…
Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as…
Colloidal dispersions are prized as model systems to understand basic properties of materials, and are central to a wide range of industries from cosmetics to foods to agrichemicals. Among the key developments in using colloids to address…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself…
We report a molecular dynamics study of the contact between a rigid solid with a randomly rough surface and an elastic block with a flat surface. We study the contact area and the interfacial separation from small contact (low load) to full…
In this paper, we analyze the effects of contact models on contact-implicit trajectory optimization for manipulation. We consider three different approaches: (1) a contact model that is based on complementarity constraints, (2) a smooth…
In this paper we discuss the relations between the exact shape of interparticle interactions in complex (dusty) plasmas and the dispersion relation of the longitudinal collective mode. Several representative repulsive potentials, predicted…
This work aims to describe a mathematical model and a numerical method to simulate a thin anisotropic composite membrane moving and deforming in 3D space under a dynamic load of an arbitrary time and space profile. The model and the method…
This paper presents a novel particle method to compute strongly coupled incompressible fluid and rigid bodies. The method adopts a velocity-based formulation and utilizes the linear complementarity problem for the incompressibility…
Contours associated to many interesting low-temperature statistical mechanics models (2D Ising model, (2+1)D SOS interface model, etc) can be described as self-interacting and self-avoiding walks on $\mathbb Z^2$. When the model is defined…
We present an analytical calculation of the hydrodynamic interaction between two spherical particles near an elastic interface such as a cell membrane. The theory predicts the frequency dependent self- and pair-mobilities accounting for the…
We study the interplay between repulsive interaction and an almost staggered on-site potential in one-dimension. Specifically, we address the Harper model for spinless fermions with nearest-neighbor repulsion, close to half-filling. Using…
A method of modelling the three-dimensional microstructure of random isotropic two-phase materials is proposed. The information required to implement the technique can be obtained from two-dimensional images of the microstructure. The…