Related papers: Nanopores -- a Versatile Tool to Study Protein Dyn…
Solid-state nanopore DNA sequencers present mechanical and chemical stability, reusability, and large-scale integrability. However, their development is hindered by the absence of a protein-free mechanism for controlling DNA translocation,…
We review the status of protein-based molecular electronics. First we discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of…
Extracellular protein concentrations and gradients queue a wide range of cellular responses, such as cell motility and division. Spatio-temporal quantification of these concentrations as produced by cells has proven challenging. As a…
Translocation through a nanopore is a new experimental technique to probe physical properties of biomolecules. A bulk of theoretical and computational work exists on the dependence of the time to translocate a single unstructured molecule…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Streaking of photoelectrons has long been used for the temporal characterization of attosecond extreme ultraviolet pulses. When the time-resolved photoelectrons originate from a coherent superposition of electronic states, they carry an…
Biomedical signals carry signature rhythms of complex physiological processes that control our daily bodily activity. The properties of these rhythms indicate the nature of interaction dynamics among physiological processes that maintain a…
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…
We elucidate the physics of the dynamical transition via 10-100ns molecular dynamics simulations at temperatures spanning 160-300K. By tracking the energy fluctuations, we show that the protein dynamical transition is marked by a cross-over…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Recent advances in protein function prediction exploit graph-based deep learning approaches to correlate the structural and topological features of proteins with their molecular functions. However, proteins in vivo are not static but…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
In this and the associated article 'BioBlender: A Software for Intuitive Representation of Surface Properties of Biomolecules', (Andrei et al) we present BioBlender as a complete instrument for the elaboration of motion (here) and the…
Despite recent breakthroughs in understanding how protein sequence relates to structure and function, considerably less attention has been paid to the general features of protein surfaces beyond those regions involved in binding and…
Single-molecule based 3rd generation DNA sequencing technologies have been explored with tremendous effort, among which nanopore sequencing is considered as one of the most promising to achieve the goal of $1,000 genome project towards…
The characterization of individual nanoparticles in a liquid constitutes a critical challenge for environmental, material, and biological sciences. To detect nanoparticles, electronic approaches are especially desirable owing to their…
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an…
Recently solid state nanopores nanogaps have generated a lot of interest in ultrafast DNA sequencing. However, there are challenges to slow down the DNA translocation process to achieve a single nucleobase resolution. A series of…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…