Related papers: The atomic-level mechanism underlying the function…
Hydrophobicity is thought to be one of the primary forces driving the folding of proteins. On average, hydrophobic residues occur preferentially in the core, whereas polar residues tends to occur at the surface of a folded protein. By…
We incorporate hydrodynamic interactions in a structure-based model of ubiquitin and demonstrate that the hydrodynamic coupling may reduce the peak force when stretching the protein at constant speed, especially at larger speeds.…
Iontronics is a burgeoning paradigm that employs ions in solution as information carriers for sensing and computing, e.g., in neuromorphic devices. The fundamentally different working principle as compared to electronics requires novel…
Microswimmers often exhibit surprising patterns due to the nonequilibrium nature of their dynamics. Collectively, suspensions of microswimmers appear as a liquid whose properties set it apart from its passive counterpart. To understand the…
The interactions of a hydrophilic surface with water can significantly influence the characteristics of the liquid water interface. In this manuscript, we explore this influence by studying the molecular structure of liquid water at a…
Biomembranes wrapping cells and organelles are not only the partitions that separate the insides but also dynamic fields for biological functions accompanied by membrane shape changes. In this review, we discuss the spatiotemporal patterns…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…
Plasmodium falciparum aquaglyceroporin (PfAQP) is a multifunctional membrane protein in the plasma membrane of P. falciparum, the parasite that causes the most severe form of malaria. The current literature has established the science of…
To explore and react to their environment, living micro-swimmers have developed sophisticated strategies for locomotion - in particular, motility with multiple gaits. To understand the physical principles associated with such a behavioural…
We perform molecular dynamics simulations of 512 water-like molecules that interact via the TIP5P potential and are confined between two smooth hydrophobic plates that are separated by 1.10 nm. We find that the anomalous thermodynamic…
Polymers are a primary building block in many biomaterials, often interacting with anisotropic backgrounds. While previous studies have considered polymer dynamics within nematic solvents, rarely are the the effects of anisotropic viscosity…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
Proteins tend to bury hydrophobic residues inside their core during the folding process to provide stability to the protein structure and to prevent aggregation. Nevertheless, proteins do expose some 'sticky' hydrophobic residues to the…
Breathing transitions represent recently discovered adsorption-induced structural transformations between large-pore and narrow-pore conformations in bistable metal-organic frameworks, such as MIL-53. We present a multiscale physical…
Fluid-structure interactions between active and passive components are important for many biological systems to function. A particular example is chromatin in the cell nucleus, where ATP-powered processes drive coherent motions of the…
The behavior of proteins near interfaces is relevant for biological and medical purposes. Previous results in bulk show that, when the protein concentration increases, the proteins unfold and, at higher concentrations, aggregate. Here, we…
We incorporate hydrodynamic interactions (HI) in a coarse-grained and structure-based model of proteins by employing the Rotne-Prager hydrodynamic tensor. We study several small proteins and demonstrate that HI facilitate folding. We also…
Mirroring their role in electrical and optical physics, two-dimensional crystals are emerging as novel platforms for fluid separations and water desalination, which are hydrodynamic processes that occur in nanoscale environments. For…
We report Molecular Dynamics (MD) simulations of a generic hydrophobic nanopore connecting two reservoirs which are initially at different Na+ concentrations, as in a biological cell. The nanopore is impermeable to water under equilibrium…
Liquid transport through nanopore is central into many applications, from water purification to biosensing or energy harvesting. Ultimately thin nanopores are of major interest in these applications to increase driving potential and reduce…