Related papers: Computing 3D chromatin configurations from contact…
Legged robot navigation in unstructured and slippery terrains depends heavily on the ability to accurately identify the quality of contact between the robot's feet and the ground. Contact state estimation is regarded as a challenging…
Inverse dynamics is used extensively in robotics and biomechanics applications. In manipulator and legged robots, it can form the basis of an effective nonlinear control strategy by providing a robot with both accurate positional tracking…
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…
Loop extrusion by motor proteins mediates the attractive interactions in chromatin on the length scale of megabases, providing the polymer with a well-defined structure and at the same time determining its dynamics. The mean square…
By means of a minimal physical model, we investigate the interplay of two phase transitions at play in chromatin organization: (1) liquid-liquid phase separation (LLPS) within the fluid solvating chromatin, resulting in the formation of…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription,…
We propose a stroboscopic method to dynamically decouple the effects of two-body atom-atom interactions for ultracold atoms, and realize a system dominated by elastic three-body interactions. Using this method, we show that it is possible…
Proteins in complex with small molecule ligands represent the core of structure-based drug discovery. However, three-dimensional representations are absent from most deep-learning-based generative models. We here present a graph-based…
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…
A molecule's 2D representation consists of its atoms, their attributes, and the molecule's covalent bonds. A 3D (geometric) representation of a molecule is called a conformer and consists of its atom types and Cartesian coordinates. Every…
Many stochastic processes in the physical and biological sciences can be modelled as Brownian dynamics with multiplicative noise. However, numerical integrators for these processes can lose accuracy or even fail to converge when the…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
Increasing evidence suggests that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space.…
In this article, we focus on the sampling of the configurational Gibbs-Boltzmann distribution, that is, the calculation of averages of functions of the position coordinates of a molecular $N$-body system modelled at constant temperature. We…
If we consider human manipulation, it is clear that contact-rich manipulation (CRM)-the ability to use any surface of the manipulator to make contact with objects-can be far more efficient and natural than relying solely on end-effectors…
The processes of Coulomb gas ordering in 3D layered system are studied by means of Brownian dynamics approach. It is found that at different densities of the carriers the 3D lattice of charges as well as new specific structures are possible…
In this communication we introduce an efficient implementation of adaptive biasing that greatly improves the speed of free energy computation in molecular dynamics simulations. We investigated the use of accelerated simulations to inform on…
In this paper, we present a coarse-grained model of DNA based on the soft ellipsoid contact potential (ECP) to evaluate the base pairing interaction properly. We extend the ellipsoid contact like potential model (ECP), suitably modified and…
For fully actuated rigid robots, kinematic inversion is a purely geometric problem, efficiently solved by closed-loop inverse kinematics (CLIK) schemes that compute joint configurations to position the robot body in space. For underactuated…