Related papers: Optimality in self-organized molecular sorting
We apply a recently developed framework for analyzing the convergence of stochastic algorithms to the general problem of large-scale nonconvex composite optimization more generally, and nonconvex likelihood maximization in particular. Our…
A molecular understanding of how protein function is related to protein structure will require an ability to understand large conformational changes between multiple states. Unfortunately these states are often separated by high free energy…
Proteins synthesized on membrane-bound ribosomes are sorted at the Golgi apparatus level for delivery to various cellular destinations: the plasma membrane or the extracellular space, and the lytic vacuole or lysosome. Sorting involves the…
Experiments show that the movement of eukaryotic cells is regulated by a process of phase separation of two competing enzymes on the cell membrane, that effectively amplifies shallow external gradients of chemical attractant. Notably, the…
Assembly theory predicts that a distinguishing signature of life is its ability to produce complex molecules in abundance, opening new possibilities for life detection. Experimental validation of this approach has so far relied on abiotic…
The movement of molecules inside living cells is a fundamental feature of biological processes. The ability to both observe and analyse the details of molecular diffusion in vivo at the single molecule and single cell level can add…
The paper is devoted to the study of a new class of optimal control problems governed by discontinuous constrained differential inclusions of the sweeping type with involving the duration of the dynamic process into optimization. We develop…
We present a new method for making diffusion models faster to sample. The method distills many-step diffusion models into few-step models by matching conditional expectations of the clean data given noisy data along the sampling trajectory.…
Molecular packing, crystallinity, and texture of semiconducting polymers are often critical to performance. Although frame-works exist to quantify the ordering, interpretations are often just qualitative, resulting in imprecise and liberal…
In the first work of this series [physics/0204035] it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the espace into…
The diffusion of active microscopic organisms in complex environments plays an important role in a wide range of biological phenomena from cell colony growth to single organism transport. Here, we investigate theoretically and…
Modern parcel logistic networks are designed to ship demand between given origin, destination pairs of nodes in an underlying directed network. Efficiency dictates that volume needs to be consolidated at intermediate nodes in typical…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Over the past decades, nonlocal models have been widely used to describe aggregation phenomena in biology, physics, engineering, and the social sciences. These are often derived as mean-field limits of attraction-repulsion agent-based…
Protein pattern formation is essential for the spatial organization of many intracellular processes like cell division, flagellum positioning, and chemotaxis. A prominent example of intracellular patterns are the oscillatory pole-to-pole…
This paper addresses the case where data come as point sets, or more generally as discrete measures. Our motivation is twofold: first we intend to approximate with a compactly supported measure the mean of the measure generating process,…
We investigate the self-organization of point-particles with short-range interactions modeled via simple 1D and 2D Hubbard-like models. We show how various properties emerge such as, boson-like ordering leading to topological structures in…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
The dynamic of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally…
The organization of cells within tissues plays a vital role in various biological processes, including development and morphogenesis. As a result, understanding how cells self-organize in tissues has been an active area of research. In our…