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The stability theorem for persistent homology is a central result in topological data analysis. While the original formulation of the result concerns the persistence barcodes of $\mathbb{R}$-valued functions, the result was later cast in a…
In this paper, we introduce multiscale persistent functions for biomolecular structure characterization. The essential idea is to combine our multiscale rigidity functions with persistent homology analysis, so as to construct a series of…
Riboswitches are structured mRNA elements that modulate gene expression. They undergo conformational changes triggered by highly specific interactions with sensed metabolites. Among the structural rearrangements engaged by riboswitches, the…
We initiate the study of stability of solutions of the 2D inviscid incompressible porous medium equation (IPM). We begin by classifying all stationary solutions of the inviscid IPM under mild conditions. We then prove some linear stability…
The efficiency of soft particles to stabilize emulsions is examined by measuring their desorption free energy, i.e., the mechanical work required to detach the particle from a fluid interface. Here, we consider rubber-like elastic as well…
Rigidity analysis using the "pebble game" can usefully be applied to protein crystal structures to obtain information on protein folding, assembly and the structure-function relationship. However, previous work using this technique has not…
We find computable criteria for stability of symplectic leaves of Poisson manifolds. Using Poisson geometry as an inspiration, we also give a general criterion for stability of leaves of Lie algebroids, including singular ones. This not…
Statistical inference for stochastic processes with time-varying spectral characteristics has received considerable attention in recent decades. We develop a nonparametric test for stationarity against the alternative of a smoothly…
Novel numerical techniques, validated by an analysis of barnase and chymotrypsin inhibitor, are used to elucidate the paramount role played by the geometry of the protein backbone in steering the folding to the correct native state. It is…
Interfacial instability is highly relevant to many important biological processes. A key example arises in wound healing experiments, which observe that an epithelial layer with an initially straight edge does not heal uniformly. We…
We utilize a multiscale modeling framework to study the effect of shape, size and ligand composition on the efficacy of binding of a ligand-coated-particle to a substrate functionalized with the target receptors. First, we show how…
Robustness of spatial pattern against perturbations is an indispensable property of developmental processes for organisms, which need to adapt to changing environments. Although specific mechanisms for this robustness have been extensively…
Growth and folding in one-layered model tissue sheets are studied in a stochastic, lattice-free single cell model which considers the discrete cellular structure of the tissue, and a coarse grained analytical approach. The polarity of the…
The mechanism by which silver staining of proteins in polyacrylamide gels interferes with mass spectrometry of peptides produced by proteolysis has been investigated. It was demonstrated that this interference increases with time between…
We investigate the formation of beta-sheet structures in proteins without taking into account specific sequence-dependent hydrophobic interactions. To accomplish this, we introduce a model which explicitly incorporates both solvation…
Semiflexible polymers are widely used as a paradigm for understanding structural phases in biomolecules including folding of proteins. Here, we compare bead-spring and bead-stick variants of coarse-grained semiflexible polymer models that…
We investigate the problem of how to obtain the force field between atoms of an experimentally determined structure. We show how this problem can be efficiently solved, even at finite temperature, where the position of the atoms differs…
We study the elasticity of fibrous materials composed of generalized stiff polymers. It is shown that in contrast to cellular foam-like structures affine strain fields are generically unstable. Instead, a subtle interplay between the…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Utilizing colloidal probe, lateral force microscopy and simultaneous confocal microscopy, combined with finite element analysis, we investigate the mechanism of static friction for a microparticle on a soft, adhesive surface. We find that…