Related papers: Energy Transfer in molecular devices
We address the problem of proteasomal protein translocation and introduce a new stochastic model of the proteasomal digestion (cleavage) of proteins. In this model we account for the protein translocation and the positioning of cleavage…
Hydrogen cations, or protons, provide the medium by which energy is stored and converted in biological systems. Such pre-eminence relies on the interplay between interfacial and bulk chemical transformations, according to mechanisms that…
MOTIVATION: Proteins fold into complex structures that are crucial for their biological functions. Experimental determination of protein structures is costly and therefore limited to a small fraction of all known proteins. Hence, different…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Understanding energy dissipation and transport in nanoscale structures is of great importance for the design of energy-efficient circuits and energy-conversion systems. This is also a rich domain for fundamental discoveries at the…
Predicting protein functional characteristics from structure remains a central problem in protein science, with broad implications from understanding the mechanisms of disease to designing novel therapeutics. Unfortunately, current machine…
We investigate the transport of proteins inside the proteasome and propose an active transport mechanism based on a spatially asymmetric interaction potential of peptide chains. The transport is driven by fluctuations which are always…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
Predicting structural and energetic properties of a molecular system is one of the fundamental tasks in molecular simulations, and it has use cases in chemistry, biology, and medicine. In the past decade, the advent of machine learning…
When a system is in equilibrium, external perturbations yield a time series of non-equilibrium distributions, and recent experimental techniques give access to the non-equilibrium data that may contain critical information. Jinwoo and…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
Biological systems are known to communicate by diffusing chemical signals in the surrounding medium. However, most of the recent literature has neglected the electron transfer mechanism occurring amongst living cells, and its role in…
The guiding and transport of energy, for example of electromagnetic waves underpins many technologies that have shaped modern society, ranging from long distance optical fibre telecommunications to on-chip optical processors. Traditionally,…
Wireless power transfer (WPT) has garnered increasing attention due to its potential to eliminate device-side batteries. With the advent of (distributed) multiple-input multiple-output (MIMO), radio frequency (RF) WPT has become feasible…
Charge transfer is a fundamental process that underlies a multitude of phenomena in chemistry and biology. Recent advances in observing and manipulating charge and heat transport at the nanoscale, and recently developed techniques for…
We study a linear chain of oscillators with inhomogeneity in their interactions with phonon bath. In a previous work on the Markovian master equation of the system, we investigated a model in which the difference in the site-phonon coupling…
Power supply for small-scale battery-powered systems such as electric vehicles (EVs and mobile robots) is being actively researched. We are particularly interested in energy management, which considers the interconnection of such systems…
Recent observations of beating signals in the excitation energy transfer dynamics of photosynthetic complexes have been interpreted as evidence for sustained coherences that are sufficiently long-lived for energy transport and coherence to…
We perform simulations to investigate how the energy carried by a molecule transfers to others in an equilibrium gas model. For this purpose we consider a microcanonical ensemble of equilibrium gas systems, each of them contains a tagged…
Following the ideas of Davydov's soliton theory, we study the bio-energy transport in protein molecules. By using a quantum Brownian motion model for a phonon dressed vibrational exciton, we calculate the time-dependence on the mean square…