Related papers: Computing 3D chromatin configurations from contact…
Involved in mitotic condensation, interaction of transcriptional regulatory elements or isolation of structural domains, understanding loop formation is becoming a paradigm in the deciphering of chromatin architecture and its functional…
We develop a comprehensive theory for the effective dynamics of Bloch electrons based on symmetry. We begin with a scheme to systematically derive the irreducible representations (IRs) characterizing the Bloch functions. Starting from a…
This paper investigates integrated localization and communication in a multi-cell system and proposes a coordinated beamforming algorithm to enhance target localization accuracy while preserving communication performance. Within this…
The square matrix-based convergence map (CM) method has proven effective in characterizing nonlinear dynamics in several 4-D dynamical systems. However, when time-dependent perturbations, such as crabbing kicks in colliders, are present, a…
A mixed basis approach based on density functional theory is employed for low dimensional systems. The basis functions are taken to be plane waves for the periodic direction multiplied by B-spline polynomials in the non-periodic direction.…
Grasping and manipulating objects is an important human skill. Since hand-object contact is fundamental to grasping, capturing it can lead to important insights. However, observing contact through external sensors is challenging because of…
Dynamic density functionals (DDFs) are popular tools for studying the dynamical evolution of inhomogeneous polymer systems. Here, we present a systematic evaluation of a set of diffusive DDF theories by comparing their predictions with data…
DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical…
The function of protein, RNA, and DNA is modulated by fast, dynamic exchanges between three-dimensional conformations. Conformational sampling of biomolecules with exact and nullspace inverse kinematics, using rotatable bonds as revolute…
Contact planning is crucial in locomoting systems.Specifically, appropriate contact planning can enable versatile behaviors (e.g., sidewinding in limbless locomotors) and facilitate speed-dependent gait transitions (e.g., walk-trot-gallop…
Combinatorial optimization problems have a broad range of applications and map to physical systems with complex dynamics. Among them, the 3-SAT problem is prominent due to its NP-complete nature. In physics terms, its solution corresponds…
Circular Dyson Brownian motion describes the Brownian dynamics of particles on a circle (periodic boundary conditions), interacting through a logarithmic, long-range two-body potential. Within the log-gas picture of random matrix theory, it…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
Contact-based motion planning for manipulation, object exploration or balancing often requires finding sequences of fixed and sliding contacts and planning the transition from one contact in the environment to another. However, most…
Contact inhibition refers to a reduction in the rate of cell migration and/or cell proliferation in regions of high cell density. Under normal conditions contact inhibition is associated with the proper functioning tissues, whereas abnormal…
The Hamiltonian for a small number, N <= 11, of bosons in a rapidly rotating harmonic trap, interacting via a short range (contact potential) or a long range (Coulomb) interaction, is studied via an exact diagonalization in the lowest…
Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop…
Results from 2.5D and 3D studies of the onset and development of the tearing instability are presented, using high fidelity resistive MHD simulations. A limited parameter study of the strength of the reconnecting field (or shear angle) was…
We study the reversible crossover between stable and bistable phases of an over-damped Brownian bead inside an optical piston. The interaction potentials are solved developing a method based on Kramers' theory that exploits the statistical…
We introduce a computationally efficient method for the automation of inverse design in science and engineering. Based on simple least-square regression, the underlying dynamic mode decomposition algorithm can be used to construct a…