Related papers: Thermodynamically Driven Signal Amplification
DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating…
Despite their topological complexity almost all functional properties of metabolic networks can be derived from steady-state dynamics. Indeed, many theoretical investigations (like flux-balance analysis) rely on extracting function from…
We present a protocol for the study of the dynamics and thermodynamics of quantum systems strongly coupled to a bath and subject to an external modulation. Our protocol quantifies the evolution of the system-bath composite by expanding the…
For multilayer materials in thin substrate systems, interfacial failure is one of the most challenges. The traction-separation relations (TSR) quantitatively describe the mechanical behavior of a material interface undergoing openings,…
Power law dynamics is used to describe the stability behavior in metabolic networks such as chemical reaction networks (CRN's). These systems allow multiple steady states within a single stoichiometric class. On the other side thermodynamic…
The dynamics of Boolean networks (BN) with quenched disorder and thermal noise is studied via the generating functional method. A general formulation, suitable for BN with any distribution of Boolean functions, is developed. It provides…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…
A number of successful theoretical models of hardness have been developed recently. A thermodynamic model of hardness, which supposes the intrinsic character of correlation between hardness and thermodynamic properties of solids, allows one…
In the development of equations of state for polyatomic molecules, thermodynamic perturbation theory (TPT) is widely used to calculate the change in free energy due to chain formation. TPT is a simplification of a more general and exact…
We investigate the thermoelectric response of single-molecule junctions composed of acyclic cross-conjugated molecules, including dendralene analogues and related iso-poly(diacetylene) (iso-PDA) motifs, in which node-possessing repeat units…
A great many observables seen in intermediate energy heavy ion collisions can be explained on the basis of statistical equilibrium. Calculations based on statistical equilibrium can be implemented in microcanonical ensemble (energy and…
Tensor-based modulation (TBM) provides a multi-linear spreading framework for blind multi-user separation in unsourced random access. In this paper, we show that TBM is a coded modulation built on a non-binary linear block code over…
In living systems, collective molecular behavior is driven by thermodynamic forces in the form of chemical gradients. Leveraging recent advances in the field of nonequilibrium physics, I show that increasing the thermodynamic force alone…
Modern thermodynamic theories can be used to study highly complex quantum dynamics. Here, we experimentally demonstrate that the violation of thermodynamic constraints allows to detect the coupling of a quantum system to a hidden…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
We investigate the thermodynamic properties of a Restricted Boltzmann Machine (RBM), a simple energy-based generative model used in the context of unsupervised learning. Assuming the information content of this model to be mainly reflected…
Complex molecules and mesoscopic structures are naturally described by general networks of elementary building blocks and tight-binding is one of the simplest quantum model suitable for studying the physical properties arising from the…
The ATLAS experiment at the Large Hadron Collider explores the use of modern neural networks for a multi-dimensional calibration of its calorimeter signal defined by clusters of topologically connected cells (topo-clusters). The Bayesian…