Related papers: Thermodynamically Driven Signal Amplification
Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…
We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…
The connection between entanglement dynamics and non-equilibrium statistics in isolated many-body quantum systems has been established both theoretically and experimentally. Many-Body Localization (MBL), a phenomenon where interacting…
Thermodynamic simulation of chemical and metallurgical systems is the only method to predict their equilibrium composition and is the most important application of chemical thermodynamics. The conventional strategy of simulation is always…
Water management is one of the most critical aspects of our society, together with population increase and climate change. Water scarcity requires a better characterization and monitoring of Water Distribution Networks (WDNs). This paper…
When we consider canonical average for classical discrete systems under constant composition (specifically, substitutional alloys) as a map phi from a set of many-body interatomic interactions to that of microscopic configuration in…
Thermalization is a ubiquitous process of statistical physics, in which details of few-body observables are washed out in favor of a featureless steady state. Even in isolated quantum many-body systems, limited to reversible dynamics,…
Thermal boundary conductance (TBC) is critical in many thermal and energy applications. A decades-old puzzle has been that many of the measured TBCs, such as those well characterized across Al/Si and ZnO/GaN interfaces, significantly exceed…
Understanding how protein mutations affect protein-nucleic acid binding is critical for unraveling disease mechanisms and advancing therapies. Current experimental approaches are laborious, and computational methods remain limited in…
Exact and approximate expressions for thermodynamic characteristics of heated matter, which consists of particles with finite mass-widths, are constructed. They are expressed in terms of Fermi/Bose distributions and spectral functions,…
The deep connection between thermodynamics, computation, and information is now well established both theoretically and experimentally. Here, we extend these ideas to show that thermodynamics also places fundamental constraints on…
Interactions between biomolecules, electrons and protons are essential to many fundamental processes sustaining life. It is therefore of interest to build mathematical models of these bioelectrical processes not only to enhance…
Molecular communication (MC) is a promising paradigm for applications where traditional electromagnetic communications are impractical. However, decoding chemical signals, especially in multi-transmitter systems, remains a key challenge due…
From the crystal structure data and using the concept of equilbrium statistical mechanics we show how to calculate the thermodynamics of protein/DNA complexes. We apply the method to the TATA-box binding protein (TBP)/TATA sequence complex.…
Due to inter-subunit communication, multisubunit enzymes usually hydrolyze ATP in a concerted fashion. However, so far the principle of this process remains poorly understood. In this study, from the viewpoint of statistical thermodynamics,…
Due to its non-crystalline nature, the glassy state has remained one the most exciting scientific challenges. To study such materials, Molecular Dynamics (MD) simulations have been extensively used because they provide a direct view into…
Ultra-precision machining of metals, the breaking of nanowires under tensile stress and fracture of nanoscale materials are examples of technologically important processes which are both extremely difficult and costly to investigate…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
Thermodynamics with internal variables is a common approach in continuum mechanics to model inelastic (i.e., non-equilibrium) material behavior. While this approach is computationally and theoretically attractive, it currently lacks a…
Chemical space is routinely explored by machine learning methods to discover interesting molecules, before time-consuming experimental synthesizing is attempted. However, these methods often rely on a graph representation, ignoring 3D…