Related papers: Glycan processing in the Golgi -- optimal informat…
The generation of two non-identical membrane compartments via exchange of vesicles is considered to require two types of vesicles specified by distinct cytosolic coats that selectively recruit cargo and two membrane-bound SNARE pairs that…
Organelle patterning and its heritability remain central mysteries in cell biology, highlighting the fundamental tension between genetic inheritance and self-assembly. Here, we explore the nonequilibrium assembly and emdedded size control…
The thesis is about an application of the shape optimization to the morphological evolution of Golgi stack. Golgi stack consists of multiple layers of cisternae. It is an organelle in the biological cells. Inspired by the Helfrich Model…
Efficient protein synthesis depends on the availability of charged tRNA molecules. With 61 different codons, shifting the balance among the tRNA abundances can lead to large changes in the protein synthesis rate. Previous theoretical work…
Glycans are the most complex biological sequence, with monosaccharides forming extended, non-linear sequences. As post-translational modifications, they modulate protein structure, function, and interactions. Due to their diversity and…
Stochasticity in gene expression gives rise to fluctuations in protein levels across a population of genetically identical cells. Such fluctuations can lead to phenotypic variation in clonal populations, hence there is considerable interest…
With the development of high throughput sequencing technology, it becomes possible to directly analyze mutation distribution in a genome-wide fashion, dissociating mutation rate measurements from the traditional underlying assumptions.…
The simulation of the metabolism in mammalian cells becomes a severe problem if spatial distributions must be taken into account. Especially the cytoplasm has a very complex geometric structure which cannot be handled by standard…
In order to produce specific complex structures from a large set of similar biochemical building blocks, many biochemical systems require high sensitivity to small molecular differences. The first and most common model used to explain this…
The mechanisms controlling the transport of proteins across the Golgi stack of mammalian and plant cells is the subject of intense debate, with two models, cisternal progression and inter-cisternal exchange, emerging as major contenders. A…
Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Clustering is a popular data mining technique that aims to partition an input space into multiple homogeneous regions. There exist several clustering algorithms in the literature. The performance of a clustering algorithm depends on its…
The boundary layer represents a fundamental structure in fluid dynamics, where accurate boundary discretization significantly enhances computational efficiency. This paper presents a third-order boundary discretization for compact…
Glycosylation is a highly complex process to produce a diverse repertoire of cellular glycans that are attached to proteins and lipids. Glycans are involved in fundamental biological processes, including protein folding and clearance, cell…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
Glycans are tree-like polymers made up of sugar monomer building blocks. They are found on the surface of all living cells, and distinct glycan trees act as identity markers for distinct cell types. Proteins called GTase enzymes assemble…
Genomic signal processing has been used successfully in bioinformatics to analyze biomolecular sequences and gain varied insights into DNA structure, gene organization, protein binding, sequence evolution, etc. But challenges remain in…
Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further enables one to potentially quantitate relevant parameters to determine the…
Particle-In-Cell codes are widely used for plasma physics simulations. It is often the case that particles within a computational cell need to be split to improve the statistics or, in the case of non-uniform meshes, to avoid the…