Related papers: Protein gradients in single cells induced by their…
Spatial heterogeneity is a hallmark of living systems, even at the molecular scale in individual cells. A key example is the partitioning of membrane-bound proteins via lipid domain formation or cytoskeleton-induced corralling. Yet the…
The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the…
We describe a simple automated method to extract and quantify transient heterogeneous dynamical changes from large datasets generated in single molecule/particle tracking experiments. Based on wavelet transform, the method transforms raw…
Cellular membranes are a heterogeneous mix of lipids, proteins and small molecules. Special groupings of saturated lipids and cholesterol form a liquid-ordered phase, known as `lipid rafts,' serving as platforms for signaling, trafficking…
Through evolution, nature has presented a set of remarkable protein materials, including elastins, silks, keratins and collagens with superior mechanical performances that play crucial roles in mechanobiology. However, going beyond natural…
Revealing the structure of complex biological macromolecules, such as proteins, is an essential step for understanding the chemical mechanisms that determine the diversity of their functions. Synchrotron based x-ray crystallography and…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
Cell sorting, whereby a heterogeneous cell mixture segregates and forms distinct homogeneous tissues, is one of the main collective cell behaviors at work during development. Although differences in interfacial energies are recognized to be…
Designing new protein structures is fundamental to computational biology, enabling advances in therapeutic molecule discovery and enzyme engineering. Existing diffusion-based generative models typically operate in Cartesian coordinate…
The origin of nonlinear responses in cells has been suggested to be crucial for various cell functions including the propagation of the nervous impulse. In physics nonlinear behavior often originates from phase transitions. Evidence for…
Protein dynamics is a fundamental element to comprehend their biological functions. However, a theoretical picture providing microscopic-detail explanation of its relevant features is still missing. One of the outmost relevant properties…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
Molecular generation and molecular property prediction are both crucial for drug discovery, but they are often developed independently. Inspired by recent studies, which demonstrate that diffusion model, a prominent generative approach, can…
Cells are constantly exposed to diverse stimuli-chemical, mechanical, or electrical-that guide their movement. In physiological conditions, these signals often overlap, as seen during infections, where neutrophils and dendritic cells…
Virtually all cells use energy and ion-specific membrane pumps to maintain large transmembrane gradients of Na$^+$, K$^+$, Cl$^-$, Mg$^{++}$, and Ca$^{++}$. Although they consume up to 1/3 of a cell's energy budget, the corresponding…
The dynamics of a folded protein is studied in water and glycerol at a series of temperatures below and above their respective dynamical transition. The system is modeled in two distinct states whereby the protein is decoupled from the bulk…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
Information processing and decision making is based upon logic operations, which in cellular networks has been well characterized at the level of transcription. In recent years however, both experimentalists and theorists have begun to…
Proteins are polymers of amino acids. These macromolecules are synthesized by intracellular machines called ribosomes. Although the experimental investigation of protein synthesis has been a traditional area of research in molecular cell…
MicroRNAs are extensively known for post-transcriptional gene regulation and pattern formation in the embryonic developmental stage. We explore the origin of these spatio-temporal patterns mathematically, considering three different motifs…