Related papers: Quantitative Determination of Spatial Protein-prot…
Crystallography may be the gold standard of protein structure determination, but obtaining the necessary high-quality crystals is also in some ways akin to prospecting for the precious metal. The tools and models developed in soft matter…
We study the (de)localization phenomena of one-component lattice fermions in spin backgrounds. The O(3) classical spin variables on sites fluctuate thermally through the ordinary nearest-neighbor coupling. Their complex two-component…
The decay behavior of the specific intensity is studied for the spatial-frequency domain imaging (SFDI). It is shown using the radiative transport equation that the decay is given by a superposition of different decay modes, and the decay…
We study the statistics of the backbone cluster between two sites separated by distance $r$ in two-dimensional percolation networks subjected to spatial long-range correlations. We find that the distribution of backbone mass follows the…
Fluorescence Lifetime Imaging Microscopy (FLIM) using multiphoton excitation techniques is now finding an important place in quantitative imaging of protein-protein interactions and intracellular physiology. We review here the recent…
This paper addresses the problem of high-resolution Doppler blood flow estimation from an ultrafast sequence of ultrasound images. Formulating the separation of clutter and blood components as an inverse problem has been shown in the…
Function of proteins or a network of interacting proteins often involves communication between residues that are well separated in sequence. The classic example is the participation of distant residues in allosteric regulation.…
Fluorescence Correlation Spectroscopy (FCS) is a powerful single-molecule technique which allows for measuring motion (diffusion, flow), concentration, and molecular interaction kinetics of fluorescent molecules from picomolar to micromolar…
A recently introduced two-channel confocal microscope with correlated detection promises up to 50% improvement in transverse spatial resolution [Simon, Sergienko, Optics Express {\bf 18}, 9765 (2010)] via the use of photon correlations.…
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open…
Finding the dense regions of a graph and relations among them is a fundamental problem in network analysis. Core and truss decompositions reveal dense subgraphs with hierarchical relations. The incremental nature of algorithms for computing…
The investigation of the static and dynamic structural properties of colloidal systems relies on techniques capable of atomic resolution in real space and femtosecond resolution in time. Recently, the cross-correlation function (CCF)…
In the context of ultra-relativistic nuclear collisions, we present a fast method for calculating the final particle spectra after the direct decay of resonances from a Cooper-Frye integral over the freeze-out surface. The method is based…
A simple theoretical framework for the description and interpretation of spatially correlated modelling residuals is presented, and the resulting tools are found to provide a useful aid to model selection in the context of weak…
We report, for the first time, a multi-confocal Fluorescence Correlation Spectroscopy (mFCS) technique which allows parallel measurements at different locations, by combining a Spatial Light Modulator (SLM), with an Electron Multiplying-CCD…
We investigate the problem of signal transduction via a descriptive analysis of the spatial organization of the complement of proteins exerting a certain function within a cellular compartment. We propose a scheme to assign a numerical…
Multidimensional separations data have the capacity to reveal detailed information about complex biological samples. However, data analysis has been an ongoing challenge in the area since the peaks that represent chemical factors may drift…
Physics has been transforming our view of nature for centuries. While combining physical knowledge with computational approaches has enabled detailed modeling of physical systems' evolution, understanding the emergence of patterns and…
For a freely evolving granular fluid, the buildup of spatial correlations in density and flow field is described using fluctuating hydrodynamics. The theory for incompressible flows is extended to the general, compressible case, including…