Related papers: Computing 3D chromatin configurations from contact…
Understanding 3d human interactions is fundamental for fine-grained scene analysis and behavioural modeling. However, most of the existing models predict incorrect, lifeless 3d estimates, that miss the subtle human contact aspects--the…
We report an approach to obtain effective pair potentials which describe the structure of two-dimensional systems of active Brownian particles. The pair potential is found by an inverse method, which matches the radial distribution function…
Knowledge of a manipulator's workspace is fundamental for a variety of tasks including robot design, grasp planning and robot base placement. Consequently, workspace representations are well studied in robotics. Two important…
We report a 3D structure-based method of predicting protein-protein interaction partners. It involves screening for pairs of tetrahedra representing interacting amino acids at the interface of the protein-protein complex, with one…
In this paper, we present an approach for generating a variety of whole-body motions for a humanoid robot. We extend the available Model Predictive Control (MPC) approaches for walking on flat terrain to plan for both vertical motion of the…
Biophysicists are modeling conformations of interphase chromosomes, often basing the strengths of interactions between segments distant on the genetic map on contact frequencies determined experimentally. Here, instead, we develop a…
The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known about the dynamics, especially in the functional states of…
We study the formation of protein-protein encounter complexes with a Langevin equation approach that considers direct, steric and thermal forces. As three model systems with distinctly different properties we consider the pairs…
The genetic instructions stored in the genome require an additional layer of information to robustly determine cell fate. This additional regulation is provided by the interplay between chromosome-patterning biochemical ("epigenetic") marks…
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…
This paper addresses the optimal time-invariant formation tracking problem with the aim of providing a distributed solution for multi-agent systems with second-order integrator dynamics. In the literature, most of the results related to…
Granular packings slowly driven towards their instability threshold are studied using a digital imaging technique as well as a nonlinear acoustic method. The former method allows us to study grain rearrangements on the surface during the…
We formulate statistical-mechanical inverse methods in order to determine optimized interparticle interactions that spontaneously produce target many-particle configurations. Motivated by advances that give experimentalists greater and…
We demonstrate a bipartition technique using a super-lattice architecture to access correlations between alternating planes of a mesoscopic array of spin-3 chromium atoms trapped in a 3D optical lattice. Using this method, we observe that…
We consider a generic representation problem of internal coordinates (bond lengths, valence angles, and dihedral angles) and their transformation to 3-dimensional Cartesian coordinates of a biomolecule. We show that the…
We present a multi-contact walking pattern generator based on preview-control of the 3D acceleration of the center of mass (COM). A key point in the design of our algorithm is the calculation of contact-stability constraints. Thanks to a…
Understanding the three-dimensional (3D) structure and stability of DNA is fundamental for its biological function and the design of novel drugs. In this study, we introduce an improved coarse-grained (CG) model, incorporating a more…
In this work, we address the question of calculating the local effective Coulomb interaction matrix in materials with strong electronic Coulomb interactions from first principles. To this purpose, we implement the constrained random phase…
We experimentally measure a three-dimensional (3D) granular system's reversibility under cyclic compression. We image the grains using a refractive-index-matched fluid, then analyze the images using the artificial intelligence of…
This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to…