Related papers: Membrane-mediated protein-protein interaction: A M…
We analyze the non-equilibrium shape fluctuations of giant unilamellar vesicles encapsulating motile bacteria. Owing to bacteria--membrane collisions, we experimentally observe a significant increase in the magnitude of membrane…
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…
Molecular dynamics simulations have revealed a dramatic increase, with increasing temperature, of the amplitude of electrostatic fluctuations caused by water at the active site of metalloprotein plastocyanin. The increased breadth of…
The adhesion of biological membranes is mediated by the binding of membrane-anchored receptor and ligand proteins. Central questions are how the binding kinetics of these proteins is affected by the membranes and by the membrane anchoring…
We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered…
Protein-protein binding enables orderly and lawful biological self-organization, and is therefore considered a miracle of nature. Protein-protein binding is steered by electrostatic forces, hydrogen bonding, van der Waals force, and…
We perform Monte Carlo simulations to study the elastic properties of the helix-coil worm-like chain model of alpha-helical polypeptides. In this model the secondary structure enters as a scalar (Ising like) variable that controls the local…
Membrane protein transporters alternate their substrate-binding sites between the extracellular and cytosolic side of the membrane according to the alternating access mechanism. Inspired by this intriguing mechanism devised by nature, we…
Deep learning models can predict protein properties with unprecedented accuracy but rarely offer mechanistic insight or actionable guidance for engineering improved variants. When a model flags an antibody as unstable, the protein engineer…
We present an implicit statistical model for the steric effect on the potential of mean force (PMF) of a molecule diffusing through a flexible nanochannel of varying size. The average cross sectional area profile of the channel and the…
A popular concept which describes the structure of polymer interfaces by ``intrinsic profiles'' centered around a two dimensional surface, the ``local interface position'', is tested by extensive Monte Carlo simulations of interfaces…
The free energy of inserting a protein into a membrane is determined by considering the variation in the spectrum of thermal fluctuations in response to the presence of a rigid inclusion. Both numerically and through a simple analytical…
The fluctuation pressure of a lipid-bilayer membrane is important for the stability of lamellar phases and the adhesion of membranes to surfaces. In contrast to many theoretical studies, which predict a decrease of the pressure with the…
Cooperativity plays an important role in the action of proteins bound to DNA. A simple, mechanical mechanism for cooperativity, in the form of a tension-mediated interaction between proteins bound to DNA at two different locations is…
Central to understanding membrane bound cell signaling is to quantify how the membrane ultra-structure consisting of transient spatial domains modulates signaling and how the signaling influences this ultra-structure. Yet, measuring the…
A microfluidic device is constructed from PDMS with a single channel having a short section that is a thin flexible membrane, in order to investigate the complex fluid-structure interaction that arises between a flowing fluid and a…
Recent experiments suggest that membranes of living cells are tuned close to a miscibility critical point in the 2D Ising universality class. We propose that one role for this proximity to criticality in live cells is to provide a conduit…
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 carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters…
We review recent simulation studies of interfaces between immiscible homopolymer phases. Special emphasis is given to the presentation of efficient simulation techniques and powerful methods of data analysis, such as the analysis of…