Related papers: Inferring Subsystem Efficiencies in Bipartite Mole…
Molecular machines consist of either a single protein or a macromolecular complex composed of protein and RNA molecules. Just like their macroscopic counterparts, each of these nano-machines has an engine that "transduces" input energy into…
Biological and living organisms sense and process information from their surroundings, typically having access only to a subset of external observables for a limited amount of time. In this work, we uncover how biological systems can…
This article focuses on the optimization of a complex system which is composed of several subsystems. On the one hand, these subsystems are subject to multiple objectives, local constraints as well as local variables, and they are…
Recent developments in nanoscale experimental techniques made it possible to utilize single molecule junctions as devices for electronics and energy transfer with quantum coherence playing an important role in their thermoelectric…
Do quantum correlations lead to better performance with respect to several different systems working independently? For quantum thermal machines, the question is whether a working medium (WM) made of $N$ constituents exhibits better…
Calculating intermolecular charge transfer integrals in organic semiconductors requires substantial computer resource for each individual calculation. We might alternatively construct a machine learning model for transfer integrals, which…
Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active…
Subdiffusion is a hallmark of complex systems, ranging from protein folding to transport in viscoelastic media. However, despite its pervasiveness, the mechanistic origins of subdiffusion remain contested. Here, we analyze both Markovian…
In this paper, we derive a number of inequalities which express power-efficiency trade-offs that hold generally for thermodynamic machines operating in non-equilibrium stationary states. One of these inequalities concerns the output power,…
Free energy calculations are at the heart of physics-based analyses of biochemical processes. They allow us to quantify molecular recognition mechanisms, which determine a wide range of biological phenomena from how cells send and receive…
Pretrained molecular encoders have become indispensable in computational chemistry for tasks such as property prediction and molecular generation. However, the standard practice of relying solely on final-layer embeddings for downstream…
The ability to perform fast and accurate atomistic simulations is crucial for advancing the chemical sciences. By learning from high-quality data, machine-learned interatomic potentials achieve accuracy on par with ab initio and…
Using an extremely large number of processing elements in computing systems leads to unexpected phenomena, such as different efficiencies of the same system for different tasks, that cannot be explained in the frame of classical computing…
This study introduces a novel approach to derive a lower bound for the entropy production rate of a subsystem by utilizing the Cauchy-Schwarz inequality. It extends to establishing comprehensive upper and lower bounds for the efficiency of…
Quantifying energy flows at nanometer scales promises to guide future research in a variety of disciplines, from microscopic control and manipulation, to autonomously operating molecular machines. A general understanding of the…
The use of machine learning to estimate the energy of a group of atoms, and the forces that drive them to more stable configurations, has revolutionized the fields of computational chemistry and materials discovery. In this domain, rigorous…
This article introduces a highly parallel algorithm for molecular dynamics simulations with short-range forces on single node multi- and many-core systems. The algorithm is designed to achieve high parallel speedups for strongly…
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…
This paper concludes a three-Part series on the limits the laws of physics place on the sustained performance of reversible computers. Part I concerned aggregate performance in terms of computational operations per unit time, but neglected…
We present an efficient method to mix well converged ab initio forces with simpler and faster ones in molecular dynamics. While the cheap forces are evaluated every time step, the converged ones correct the trajectory only every n time…