Related papers: Lattice models for protein organization throughout…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
The structural properties of packed soft-core particles provide a platform to understand the cross-pollinated physical concepts in solid-state- and soft-matter physics. Confined on spherical surface, the traditional differential geometry…
The recent discovery of a lateral organization in cell membranes due to small structures called 'rafts' has motivated a lot of biological and physico-chemical studies. A new experiment on a model system has shown a spectacular budding…
Elastic interactions arising from a difference of lattice spacing between two coherent phases can have a strong influence on the phase separation (coarsening) of alloys. If the elastic moduli are different in the two phases, the elastic…
Important cellular processes, such as cell motility and cell division, are coordinated by cell polarity, which is determined by the non-uniform distribution of certain proteins. Such protein patterns form via an interplay of protein…
The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
Cellular membranes are elastic lipid bilayers that contain a variety of proteins, including ion channels, receptors, and scaffolding proteins. These proteins are known to diffuse in the plane of the membrane and to influence the bending of…
Fluorescence microscopy has led to impressive quantitative models and new insights gained from richer sets of biomedical imagery. However, there is a dearth of rigorous and established bioimaging strategies for modeling spatiotemporal…
Many transport processes in nature take place on substrates, often considered as unidimensional lanes. These unidimensional substrates are typically non-static: affected by a fluctuating environment, they can undergo conformational changes.…
Magnetic fluids are colloidal suspensions of ferromagnetic particles covered with a surfactant layer, dispersed in a host liquid. The existence of cooperative phenomena in such magnetic colloidal systems, makes the determining of their…
We present a multi-phase design parameterization to obtain optimized heterogeneous lattice structures. The 3D domain is discretized into a cubical grid wherein each cube has eight distinct unit cell types or phases. When all phases are…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
We study analytically the dynamics and the micro-structural changes of a host medium caused by a driven tracer particle moving in a confined, quiescent molecular crowding environment. Imitating typical settings of active micro-rheology…
We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…
Two-dimensional colloidal suspensions exposed to periodic external fields exhibit a variety of molecular crystalline phases. There two or more colloids assemble at lattice sites of potential minima to build new structural entities, referred…
Motivated by lattice mixture identification and grain boundary detection, we present a framework for lattice pattern representation and comparison, and propose an efficient algorithm for lattice separation. We define new scale and shape…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
Collective behavior of proteins on biomembranes is usually studied within the spontaneous curvature model. Here we consider an alternative phenomenological approach, which accounts consistently for partial ordering of proteins as well as…
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…