Related papers: Engineering Nanoscale Biological Molecular Motors
Dynamics of molecular motors that move along linear lattices and interact with them via reversible destruction of specific lattice bonds is investigated theoretically by analyzing exactly solvable discrete-state ``burnt-bridge'' models.…
The present level of development of molecular force field methods is assessed from the point of view of simulation-based engineering, outlining the immediate perspective for further development and highlighting the newly emerging discipline…
Molecule- and solid-state gears build the elementary constituents of nanoscale mechanical machineries. Recent experimental advances in fabrication technologies in the field have strongly contributed to better delineate the roadmap towards…
We classify research fields in biology into those on flows of materials, energy, and information. As a representative energy transducing machinery in biology, our research target, V1-ATPase from a bacterium Enterococcus hirae, a typical…
The genetic blueprint for the essential functions of life is encoded in DNA, which is translated into proteins -- the engines driving most of our metabolic processes. Recent advancements in genome sequencing have unveiled a vast diversity…
A molecular rotor mechanism is proposed to explain weak magnetic field effects in biology. Despite being nanoscale (1 nm), this rotor exhibits quantum superposition and interference. Analytical modeling shows its quantum dynamics are highly…
This study explores the transformative potential of nanocatalysts, emphasizing their pivotal role in catalysis and material science. Key synthesis techniques, including chemical reduction and hybrid methods, are highlighted for their…
Biological molecular machines are bifunctional enzymes that catalyze two processes: one donating free energy and the other accepting it. Recent studies show that most protein enzymes have rich stochastic dynamics of transitions between the…
Biology-derived algorithms are an important part of computational sciences, which are essential to many scientific disciplines and engineering applications. Many computational methods are derived from or based on the analogy to natural…
Nature has developed striking light-powered proteins such as bacteriorhodopsin, which can convert light energy into conformational changes for biological functions. Such natural machines are a great source of inspiration for creation of…
This paper presents a molecular mechanics study for new nanorobotic structures using molecular dynamics (MD) simulations coupled to virtual reality (VR) techniques. The operator can design and characterize through molecular dynamics…
Single molecular rotor is an important component for constructing bot-tom-up molecular mechanical machines and a window for shedding light on complex physical and chemical questions about motions of organic molecules on surfaces. Stability…
Molecular machines are stochastic systems that catalyze the energetic processes keeping living cells alive and structured. Inspired by the examples of F1-ATP synthase and the bacterial flagellum, we present a minimal model of an externally…
Despite significant fluctuation under thermal noise, biological machines in cells perform their tasks with exquisite precision. Using molecular simulation of a coarse-grained model and theoretical arguments we envisaged how kinesin, a…
Biochars have been attracting renewed attention as economical and environmentally friendly carbon sequestration materials with a diverse range of applications. However, experimental developments may be limited by the lack of molecular-level…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Most computer simulations of molecular dynamics take place under equilibrium conditions--in a closed, isolated system, or perhaps one held at constant temperature or pressure. Sometimes, extra tensions, shears, or temperature gradients are…
The generation of unidirectional motion has been a long-standing challenge in engineering of molecular motors and, more generally, machines. A molecular motor is characterized by a set of low energy states that differ in their…
The molecular machinery of life is largely created via self-organisation of individual molecules into functional assemblies. Minimal coarse-grained models, where a whole macromolecule is represented by a small number of particles, can be of…
Molecular motors power directed transport of cargoes within cells. Even if a single motor is sufficient to transport a cargo, motors often cooperate in small teams. We discuss the cooperative cargo transport by several motors theoretically…