相关论文: Engines at molecular scales
Transport of intracellular cargo is often mediated by teams of molecular motors that function in a chaotic environment under varying conditions. We show that the motors have unique steady state behavior which enables transport modalities…
Stochasticity (or noise) at cellular and molecular levels has been observed extensively as a universal feature for living systems. However, how living systems deal with noise while performing desirable biological functions remains a major…
This thesis focuses on three fundamental aspects of biological systems; namely, entropy production, Bayesian mechanics, and the free-energy principle. The contributions are threefold: 1) We compute the entropy production for a greater class…
Understanding how the effectiveness of natural photosynthetic energy harvesting systems arises from the interplay between quantum coherence and environmental noise represents a significant challenge for quantum theory. Recently it has begun…
We study a Brownian motor driven by a colored non Gaussian noise source with a $q$-dependent probability distribution, where $q$ is a parameter indicating the departure from Gaussianity. For $q=1$ the noise is Gaussian…
Transport of a Brownian particle moving along the axis of a three-dimensional asymmetric periodic tube is investigated in the presence of asymmetric unbiased forces. The reduction of the coordinates may involve not only the appearance of…
In living cells, molecular motors convert chemical energy into mechanical work. Its thermodynamic energy efficiency, i.e. the ratio of output mechanical work to input chemical energy, is usually high. However, using two-state models, we…
Biological systems are notoriously noisy. Noise, therefore, also plays an important role in many models of neural impulse generation. Noise is not only introduced for more realistic simulations but also to account for cooperative effects…
We revealed a right-left asymmetry of the inter-well mean first passage times for the Brownian particles in a ratchet potential under internal white noise. We showed analytically and numerically that this asymmetry gives rise to the…
The stochastic driving force exerted by a single molecular motor (e.g., a kinesin, or myosin) moving on a periodic molecular track (microtubule, actin filament, etc.) is discussed from a general viewpoint open to experimental test. An…
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.…
In this work we study the assisted translocation of a polymer across a membrane nanopore, inside which a molecular motor exerts a force fuelled by the hydrolysis of ATP molecules. In our model the motor switches to its active state for a…
Simulations can help unravel the complicated ways in which molecular structure determines function. Here, we use molecular simulations to show how slight alterations of a molecular motor's structure can cause the motor's typical dynamical…
In this thesis we aim to analyze and quantify the energetic and information contents that can be extracted from a dynamical system subject to the external environment. The latter is usually assumed to be deleterious for the feasibility of…
We present a generalized energy-depot model in which the conversion rate of the internal energy into motion can be dependent on the position and the velocity of a particle. When the conversion rate is a general function of the velocity, the…
Living cells are known to generate non-Gaussian active fluctuations significantly larger than thermal fluctuations owing to various active processes. Understanding the effect of these active fluctuations on various physicochemical…
Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…
The operation of Brownian motors is usually described in terms of out-of-equilibrium and symmetry-breaking settings, with the relevant spatiotemporal symmetries identified from the analysis of the equations of motion for the system at hand.…
The traffic of molecular motors through open tube-like compartments is studied using lattice models. These models exhibit boundary-induced phase transitions related to those of the asymmetric simple exclusion process (ASEP) in one…
Molecular machines described in this paper are meant to be such molecular systems that make use of conformational mobility (i.e. hindered rotation around chemical bonds and molecular construction deformations with formation and breakage of…