Related papers: Computing 3D chromatin configurations from contact…
By observing reconstituted chromatin by fluorescence microscopy (FM) and atomic force microscopy (AFM), we found that the density of nucleosomes exhibits a bimodal profile, i.e., there is a large transition between the dense and dispersed…
The electron and photon transport processes in spectroscopy techniques described by the invariant embedding theory is here revisited. We report a convergence method to obtain closed analytical solutions to the 3D integro-differential…
3D grasp synthesis generates grasping poses given an input object. Existing works tackle the problem by learning a direct mapping from objects to the distributions of grasping poses. However, because the physical contact is sensitive to…
This paper presents a novel contact-implicit trajectory optimization method using an analytically solvable contact model to enable planning of interactions with hard, soft, and slippery environments. Specifically, we propose a novel contact…
Short-range interactions and long-range contacts drive the 3D folding of structured proteins. The proteins' structure has a direct impact on their biological function. However, nearly 40% of the eukaryotes proteome is composed of…
Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites…
Current models for the folding of the human genome see a hierarchy stretching down from chromosome territories, through A/B compartments and TADs (topologically-associating domains), to contact domains stabilized by cohesin and CTCF.…
We employ the diffusing transcription factors model for numerical simulation of chromatin topology conformations and transcriptional processes of human chromatin. Simulations of a short chromatin filament reveal different possible pathways…
How genes affect tissue scale organization remains a longstanding biological puzzle. As experimental efforts aim to quantify gene expression, chromatin organization, cellular structure, and tissue structure, computational modeling lags…
Accurate uncertainty estimation associated with the pose transformation between two 3D point clouds is critical for autonomous navigation, grasping, and data fusion. Iterative closest point (ICP) is widely used to estimate the…
The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific,…
Recent progress has been made in the understanding of the physical properties of chromatin -- the dense complex of DNA and histone proteins that occupies the nuclei of plant and animal cells. Here I will focus on the two lowest levels of…
This paper evaluates state-of-the-art contact models at predicting the motions and forces involved in simple in-hand robotic manipulations. In particular it focuses on three primitive actions --linear sliding, pivoting, and rolling-- that…
We propose a model for the formation of chromatin loops based on the diffusive sliding of a DNA-bound factor which can dimerise to form a molecular slip-link. Our slip-links mimic the behaviour of cohesin-like molecules, which, along with…
This article reviews recent inverse statistical-mechanical methodologies that we have devised to optimize interaction potentials in soft matter systems that correspond to stable "target" structures. We are interested in finding the…
In the paper we investigate statistical and topological properties of fractional Brownian polymer chains, equipped with the short-range volume interactions. The attention is paid to statistical properties of collapsed conformations with the…
Background: Ab initio many-body methods have been developed over the past ten years to address mid-mass nuclei... As progress in the design of inter-nucleon interactions is made, further efforts must be made to tailor many-body methods.…
We propose a novel and efficient lifting approach for the optimal control of rigid-body systems with contacts to improve the convergence properties of Newton-type methods. To relax the high nonlinearity, we consider the state, acceleration,…
An approximate approach to quantum vibrational dynamics, "Brownian Chain Molecular Dynamics (BCMD)", is proposed to alleviate the chain resonance and curvature problems in the imaginary time-based path integral (PI) simulation. Here the…
For one-dimensional systems with delta-contact interactions, the convergence of the exact-diagonalization method is tested with a basis of harmonic oscillator eigenfunctions with frequency $\Omega$ optimized through the minimization of the…