Related papers: The free energy requirements of biological organis…
We derive the bias function that minimizes the statistical error of free energy differences calculated in work-biased fast-switching simulations. The optimum bias function is compared to other bias functions using a particle pulled through…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
Free energy calculation is critical in predictive tasks such as protein folding, docking and design. However, rigorous calculation of free energy change is prohibitively expensive in these practical applications. The minimum potential…
The evaluation of the minimal evolution time between two distinguishable states of a system is important for assessing the maximal speed of quantum computers and communication channels. Lower bounds for this minimal time have been proposed…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
We consider the thermodynamic properties of systems in contact with an information source and focus on the consequences of energetic cost associated with the exchange of information. To this end we introduce the model of a thermal tape and…
Physical systems driven away from equilibrium by an external controller dissipate heat to the environment; the excess entropy production in the thermal reservoir can be interpreted as a "cost" to transform the system in a finite time. The…
Entropy is one of the key thermodynamic variables reflecting changes in the state of matter. Unlike other thermodynamic variables, it is well-defined also for nonequilibrium steady states through its relation to information. Applying this…
Micro- and nano-scale systems driven by rapid changes in control parameters (control protocols) dissipate significant energy. In the fast-protocol limit, we find that protocols that minimize dissipation at fixed duration are universally…
When a system is driven out of equilibrium by a time-dependent protocol that modifies the Hamiltonian, it follows a nonequilibrium path. Samples of these paths can be used in nonequilibrium work theorems to estimate equilibrium quantities,…
Molecular motors play pivotal roles in organizing the interior of cells. A motor efficient in cargo transport would move along cytoskeletal filaments with a high speed and a minimal error in transport distance (or time) while consuming a…
This thesis is devoted to the theoretical study of slow thermodynamic processes in non-equilibrium stochastic systems. Its main result is a physically and mathematically consistent construction of relevant thermodynamic quantities in the…
Quantifying the flow of energy within and through fluctuating nanoscale systems poses a significant challenge to understanding microscopic biological machines. A common approach involves coarse-graining, which allows a simplified…
We briefly address Landauer's Principle and some related issues in thermal demons. We show that an error-free Turing computer works in the zero-entropy limit, which proves Landauer's derivation incorrect. To have a physical logic gate,…
The theoretical and experimental study of energy transfer in photosynthesis has revealed an interesting transport regime, which lies at the borderline between classical transport dynamics and quantum-mechanical interference effects.…
A novel thermodynamic integration (TI) scheme is presented that allows computing the free energy of grain boundaries (GBs) in crystals from atomistic computer simulation. Unlike previous approaches, the method can be applied at arbitrary…
The Landauer principle states that any logically irreversible information processing must be accompanied by dissipation into the environment. In this study, we investigate the heat dissipation associated with finite-time information erasure…
We formulate the computational processes of perception in the framework of the principle of least action by postulating the theoretical action as a time integral of the free energy in the brain sciences. The free energy principle is…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
Many physical, biological, and even social systems are faced with the problem of how to efficiently harvest free energy from an environment that can have many possible states, yet only have a limited number of harvesting protocols to choose…