Related papers: Kinetics of seeded protein aggregation: theory and…
Many biological systems can be described by finite Markov models. A general method for simplifying master equations is presented that is based on merging adjacent states. The approach preserves the steady-state probability distribution and…
When applying automatic analysis of fluorescence or histopathological images of cells, it is necessary to partition, or de-clump, partially overlapping cell nuclei. In this work, I describe a method of partitioning partially overlapping…
It is proposed that the co-expression of statistically significant motifs among the sequences of a proteome is a phylogenetic trait. From the co-expression matrix of such motifs in a group of prokaryotic proteomes a suitable definition of a…
Specific protein-protein interactions are crucial in the cell, both to ensure the formation and stability of multi-protein complexes, and to enable signal transduction in various pathways. Functional interactions between proteins result in…
We introduce a collection of complex networks generated by a combination of preferential attachment and a previously unexamined process of "splitting" nodes of degree $k$ into $k$ nodes of degree 1. Four networks are considered, each…
We introduce HITMIX, a new technique for network seed-set expansion, i.e., the problem of identifying a set of graph vertices related to a given seed-set of vertices. We use the moments of the graph's hitting-time distribution to quantify…
We consider pattern formation in a sheared dense mixture of cohesive and non-cohesive grains. Our findings show that cohesive grains, which would typically form distributed agglomerates, instead segregate into percolating stripes or layers…
A plethora of natural and industrial shear-driven granular flows exhibit particle-size segregation. Its occurrence is commonly attributed to two primary mechanisms: kinetic sieving and squeeze expulsion. While kinetic sieving is relatively…
In a recent paper (Gonzalez et al., 2023), we investigated the motion of grains within a granular bed sheared by a viscous fluid, and showed how segregation and hardening occur in the fluid- (bedload) and solid-like (creep) regions. In this…
Significant progress in computer hardware and software have enabled molecular dynamics (MD) simulations to model complex biological phenomena such as protein folding. However, enabling MD simulations to access biologically relevant…
Despite the constant evolution of similarity searching research, it continues to face the same challenges stemming from the complexity of the data, such as the curse of dimensionality and computationally expensive distance functions.…
The conformational landscape of proteins is crucial to understanding their functionality in complex biological processes. Traditional physics-based computational methods, such as molecular dynamics (MD) simulations, suffer from rare event…
Processes that proceed reliably from a variety of initial conditions to a unique final form, regardless of moderately changing conditions, are of obvious importance in biophysics. Protein folding is a case in point. We show that the action…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
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…
Protein aggregation occurs when misfolded or unfolded proteins physically bind together, and can promote the development of various amyloid diseases. This study aimed to construct surrogate models for predicting protein aggregation via…
Probing the reaction mechanisms of supramolecular processes in soft- and biological matter, such as protein aggregation, is inherently challenging. These processes emerge from the simultaneous action of multiple molecular mechanisms, each…
In this paper, an automatic seeded region growing algorithm is proposed for cellular image segmentation. First, the regions of interest (ROIs) extracted from the preprocessed image. Second, the initial seeds are automatically selected based…
We propose an application of molecular information theory to analyze the folding of single domain proteins. We analyze results from various areas of protein science, such as sequence-based potentials, reduced amino acid alphabets, backbone…
Branched actin networks at the leading edge of a crawling cell evolve via protein-regulated processes such as polymerization, depolymerization, capping, branching, and severing. A formulation of these processes is presented and analyzed to…