Related papers: Computational modeling of biological nanopores
Nanopores attracted a great deal of scientific interest as templates for biological sensors as well as model systems to understand transport phenomena at the nanoscale. The experimental and theoretical analysis of nanopores has been so far…
Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a…
Macroscopic strain experiments revealed that Si crystals traversed by parallel, channel-like nanopores functionalized with the muscle polymer polypyrrole exhibit large and reversible electrochemo-mechanical actuation in aqueous…
Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…
We investigated the translation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compared the mobilities with those obtained from previous coarse-grained equilibrium…
In living systems, we often see the emergence of the ingredients necessary for computation -- the capacity for information transmission, storage, and modification -- begging the question of how we may exploit or imitate such biological…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
In a multiscale modeling approach, we present computer simulation results for a rectifying bipolar nanopore on two modeling levels. In an all-atom model, we use explicit water to simulate ion transport directly with the molecular dynamics…
Advanced nanopore measurements allow structural probing of molecules with high spatial and temporal resolution. We report high signal-to-noise, 1-10 MHz bandwidth, translocation measurements of the multi-state folding of heme protein…
Since the first measurement of electron tunneling through an organic monolayer in 1971,(Mann and Kuhn, 1971) and the gedanken experiment of a molecular current rectifying diode in 1974,(Aviram and Ratner, 1974) molecular-scale electronics…
While the fundamental principles of light-matter interaction are well-understood and drive countless technologies, the world of multiphoton processes remains a fascinating puzzle, holding the potential to drastically alter our understanding…
Neural probes are in vivo invasive devices that combine electrophysiology and optogenetics to gain insight into how the brain operates, down to the single neuron and its network activity. Their integration of stimulation sites and sensors…
Dielectrophoresis (DEP), the motion of polarizable particles in non-uniform electric fields, has become an important tool for the transport, separation, and characterization of microparticles in biomedical and nanoelectronics research. In…
Janus --or two-sided, charged membranes offer promise as ionic current rectifiers. In such systems, pores consisting of two regions of opposite charge can be used to generate a current from a gradient in salinity. The efficiency of…
Ion transporters in Nature exhibit a wealth of complex transport properties such as voltage gating, activation, and mechanosensitive behavior. When combined, such processes result in advanced ionic machines achieving active ion transport,…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
Solid-state nanopores are promising tools for single molecule detection of both DNA and proteins. In this study, we investigate the patterns of ionic current blockades as DNA translocates into or out of the geometric confinement of such…
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA…
Based on modern single molecule techniques, we devise a number of possible experimental setups to probe local properties of DNA such as the presence of DNA-knots, loops or folds, or to obtain information on the DNA-sequence. Similarly, DNA…
We demonstrate simultaneous measurements of DNA translocation into glass nanopores using ionic current detection and fluorescent imaging. We verify the correspondence between the passage of a single DNA molecule through the nanopore and the…