Related papers: Elastohydrodynamics and kinetics of protein patter…

Adaptation of the chemotaxis sensory pathway of the bacterium Escherichia coli is integral for detecting chemicals over a wide range of background concentrations, ultimately allowing cells to swim towards sources of attractant and away from…

Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…

Shape had been intuitively recognized to play a dominant role in determining the global motion patterns of bio-molecular assemblies. However, it is not clear exactly how shape determines the motion patterns. What about the local…

We report a numerical simulation of the phase diagram of a simple model for membrane proteins constrained to move in a plane. In analogy with the corresponding three dimensional models, the liquid-gas transition becomes metastable as the…

A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…

Predicting the physical interaction of proteins is a cornerstone problem in computational biology. New classes of learning-based algorithms are actively being developed, and are typically trained end-to-end on protein complex structures…

Active networks made of biopolymers and motor proteins are valuable bioinspired systems that have been used in the last decades to study the cytoskeleton and its self-organization under mechanical stimulation. Different techniques are…

Biological systems have evolved to amazingly complex states, yet we do not understand in general how evolution operates to generate increasing genetic and functional complexity. Molecular recognition sites are short genome segments or…

In neuroscience, synaptic plasticity refers to the set of mechanisms driving the dynamics of neuronal connections, called synapses and represented by a scalar value, the synaptic weight. A Spike-Timing Dependent Plasticity (STDP) rule is a…

Experiments have revealed that membrane proteins can form two-dimensional clusters with regular translational and orientational protein arrangements, which may allow cells to modulate protein function. However, the physical mechanisms…

Kinetic Particle In Cell (PIC) methods can extend greatly their range of applicability if implicit time differencing and spatial adaption are used to address the wide range of time and length scales typical of plasmas. For implicit…

Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…

In the post-Moore era, the need for efficient solutions to non-deterministic polynomial-time (NP) problems is becoming more pressing. In this context, the Ising model implemented by the probabilistic computing systems with probabilistic…

It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range…

We investigate the convergence of solutions of a recently proposed diffuse interface/phase field model for cell blebbing by means of matched asymptotic expansions. It is a biological phenomenon that increasingly attracts attention by both…

Elastic network models (ENM) and constraint-based, topological rigidity analysis are two distinct, coarse-grained approaches to study conformational flexibility of macromolecules. In the two decades since their introduction, both have…

The relation between thermal fluctuations and the mechanical response of a free membrane has been explored in great detail, both theoretically and experimentally. However, understanding this relationship for membranes, locally pinned by…

In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…

Protein-peptide interactions play essential functional roles in living organisms and their structural characterization is a hot subject of current experimental and theoretical research. Computational modeling of the structure of…

Intermolecular interactions in protein solutions in general contain many contributions. If short-range attractions dominate, the state diagram exhibits liquid-liquid phase separation (LLPS) that is metastable with respect to…