Related papers: Evolution and Mutations of Beta 2 Microglobulin
A finite element method for the evolution of a two-phase membrane in a sharp interface formulation is introduced. The evolution equations are given as an $L^2$--gradient flow of an energy involving an elastic bending energy and a line…
Our previous molecular dynamic simulation studies of simple two-dimensional (2D) systems \cite{matt_big} suggested that both geometrical defects (localized, large-amplitude deviations from hexagonal ordering) and topological defects…
Inverted solubility--a crystal melting upon cooling--is observed in a handful of proteins, such as carbomonoxy hemoglobin and $\gamma$D-crystallin. In human $\gamma$D-crystallin, the phenomenon is associated with the mutation of the…
The elastic properties of two-component bilayer membranes are studied using a coarse grain model for amphiphilic molecules. The two species of amphiphiles considered here differ only in their length. Molecular Dynamics simulations are…
We propose a hybrid dynamical system approach to model the evolution of a pathogen that experiences different selective pressures according to a stochastic process. In every environment, the evolution of the pathogen is described by a…
T cells use sophisticated shape dynamics (morphodynamics) to migrate towards and neutralise infected and cancerous cells. However, there is limited quantitative understanding of the migration process in 3D extracellular matrices (ECMs) and…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
Mesozooplankton aggregations undergoing vertical migrations in the upper ocean have been hypothesized to have an important role in the redistribution of carbon, nutrients, and oxygen via biogenic hydrodynamic transport (BHT). While…
Ever since the raft model for biomembranes has been proposed, the traditional view of biomembranes based on the fluid-mosaic model has been altered. In the raft model, dynamical heterogeneities in multi-component lipid bilayers play an…
Studies of coevolution of amino acids within and between proteins have revealed two types of coevolving units: coevolving contacts, which are pairs of amino acids distant along the sequence but in contact in the three-dimensional structure,…
Upon heating, egg yolk transforms from a liquid to a gel due to protein denaturation. This process can serve as a useful model to better understand protein denaturation in general. Using x-ray holographic tomography, we investigated the…
Biological membranes mainly consist of lipids and proteins. While the proteins have many functions as single molecules, the membrane as a whole displays physical properties that cannot be explained on the single molecule level. For example,…
Learning to change shape is a fundamental strategy of adaptation and evolution of living organisms, from bacteria and cells to tissues and animals. Human-made materials can also exhibit advanced shape morphing capabilities, but lack the…
A cosmological multidimensional hydrodynamic code is described and tested. This code is based on modern high-resolution shock-capturing techniques. It can make use of a linear or a parabolic cell reconstruction as well as an approximate…
Development, regeneration and cancer involve drastic transitions in tissue morphology. In analogy with the behavior of inert fluids, some of these transitions have been interpreted as wetting transitions. The validity and scope of this…
The one-dimensional non-boost-invariant evolution of the quark-gluon plasma, presumably produced during the early stages of heavy-ion collisions, is analyzed within the frameworks of viscous and anisotropic hydrodynamics. We neglect…
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…
We investigated melting transitions in biological membranes in their native state that include their membrane proteins. These membranes originated from \textit{E. coli}, \textit{B. subtilis}, lung surfactant and nerve tissue from the spinal…
We investigate the formation of beta-sheet structures in proteins without taking into account specific sequence-dependent hydrophobic interactions. To accomplish this, we introduce a model which explicitly incorporates both solvation…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…