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More than a century has passed since van't Hoff and Arrhenius formulated their celebrated rate theories, but there are still elusive aspects in the temperature-dependent phase transition kinetics of molecular systems. Here I present a…
Subdiffusion has been proposed as an explanation of various kinetic phenomena inside living cells. In order to fascilitate large-scale computational studies of subdiffusive chemical processes, we extend a recently suggested mesoscopic model…
Atomic and single-molecule junctions represent the ultimate limit to the miniaturization of electrical circuits. They are also ideal platforms to test quantum transport theories that are required to describe charge and energy transfer in…
The energetics of the stochastic process has shown the balance of energy on the mesoscopic level. The heat and the energy defined there are, however, generally different from their macroscopic counterpart. We show that this discrepancy can…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
Reaction systems are a computational model inspired by the bio-chemical reactions that happen inside biological cells. They have been and currently are studied for their many nice theoretical properties. They are also a useful modeling tool…
The macroscopic behavior of the solution of a coupled system of partial differential equations arising in the modeling of reaction-diffusion processes in periodic porous media is analyzed. Our mathematical model can be used for studying…
We propose a novel molecular device that pumps heat against a thermal gradient. The system consists of a molecular element connecting two thermal reservoirs that are characterized by different spectral properties. The pumping action is…
Characterizing quantum phases-of-matter at finite-temperature is essential for understanding complex materials and large-scale thermodynamic phenomena. Here, we develop algorithmic protocols for simulating quantum thermodynamics on quantum…
Thermal emission is the radiation of electromagnetic waves from hot objects. The promise of thermal-emission engineering for applications in energy harvesting, radiative cooling, and thermal camouflage has recently led to renewed research…
The energy dissipated by a living organism is commonly identified with heat generation. However, as cells exchange metabolites with their environment they also dissipate energy in the form of chemical entropy. How dissipation is distributed…
The aim of this study was to evaluate and compare temperature distributions for different tissues being treated at the time of interstitial microwave hyperthermia. A coaxial-slot antenna implemented into the tissue is the source of…
It was once purported that biological systems were far too warm and wet to support quantum phenomena mainly due to thermal effects disrupting quantum coherence. However recent experimental results and theoretical analyses have shown that…
The process of thermalization in many-body systems is driven by complex interactions among sub-systems and with the surrounding environment. Here we lay the theoretical foundations for the active control of local thermal states in arbitrary…
Classical thermodynamics is unrivalled in its range of applications and relevance to everyday life. It enables a description of complex systems, made up of microscopic particles, in terms of a small number of macroscopic quantities, such as…
The concept of entropy has been pivotal in the formulation of thermodynamics. For systems driven away from thermal equilibrium, a comparable role is played by entropy production and dissipation. Here we provide a comprehensive picture how…
The integration time step is a critical determinant of performance in molecular dynamics simulations, governing the trade-off between speed and fidelity. Although 2 fs remains the standard in atomistic biomolecular simulations, the push for…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
Currently, biological signaling is envisaged as a combination of activation and movement, triggered by local molecular interactions and molecular diffusion, respectively. However, we here suggest, that other fundamental physical mechanisms…