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Alzheimer's Disease Analysis Model (ADAM) is a multi-agent reasoning large language model (LLM) framework designed to integrate and analyze multimodal data, including microbiome profiles, clinical datasets, and external knowledge bases, to…
This paper provides the first ab-initio on-the-fly example of using the Quasi-Diabatic (QD) scheme for non-adiabatic simulations with diabatic dynamics approaches. The QD scheme provides a seamless interface between diabatic quantum…
We give an example of a simple mechanical system described by the generalized harmonic oscillator equation, which is a basic model in discussion of the adiabatic dynamics and geometric phase. This system is a linearized plane pendulum with…
Proteins typically exist in complexes, interacting with other proteins or biomolecules to perform their specific biological roles. Research on single-chain protein modeling has been extensively and deeply explored, with advancements seen in…
Douglas-Rachford splitting and its equivalent dual formulation ADMM are widely used iterative methods in composite optimization problems arising in control and machine learning applications. The performance of these algorithms depends on…
The Adomian Decomposition Method (ADM) is a very effective approach for solving broad classes of nonlinear partial and ordinary differential equations, with important applications in different fields of applied mathematics, engineering,…
Background: Type 2 diabetes mellitus (T2DM) is increasingly recognised as a systemic disease characterised by coordinated dysfunction across metabolic, renal, lipid, and inflammatory pathways. Existing clinical assessments often fail to…
Surface hopping algorithms, as an important class of quantum dynamics simulation algorithms for non-adiabatic dynamics, are typically performed in the adiabatic representation, which can break down in the presence of ill-defined adiabatic…
We consider an open quantum system described by a Lindblad-type master equation with two times-scales. The fast time-scale is strongly dissipative and drives the system towards a low-dimensional decoherence-free space. To perform the…
We consider slowly evolving, i.e. ADIABATIC, operational regime within a transmission level (continental scale) natural gas pipeline system. This allows us to introduce a set of nodal equations of reduced complexity describing gas…
In this paper, we continue the development of a generic adiabatic scheme for nonlinear evolutions. We consider an abstract gradient flow of some energy functional, together with a given manifold of static solutions arising from broken…
Mixed-quantum-classical molecular dynamics simulation implies an effective measurement on the electronic states owing to continuously tracking the atomic forces.Based on this insight, we propose a quantum trajectory mean-field approach for…
This paper presents a complete closed-form analytical model for determining the per-cycle energy consumption of stepwise adiabatic drivers used for driving a capacitive load such as a power FET gate. The model takes into account the number…
Nonadiabatic molecular dynamics (NAMD) is widely used to describe hot electron relaxation and nonradiative recombination processes, but high computational costs limit its application to large supercells. Here, we implement a nonadiabatic…
We investigate the dynamical and structural properties of absorbing phase transitions (APTs) within granular systems. Specifically, we examine a model for vibrofluidized systems of spherical grains, which undergo a transition from a state…
We present a whole-body model of human metabolism that utilizes a system of organs and blood vessels to simulate the enzymatic reactions. The model focuses on key organs, including the brain, heart and lungs, liver, gut, and kidney, as well…
The geometric (Berry) phase of a two-level system in a dissipative environment is analyzed by using the second-quantized formulation, which provides a unified and gauge-invariant treatment of adiabatic and nonadiabatic phases and is thus…
The one-dimensional kinetic contact process with parallel update is introduced and studied by the mean-field approximation and Monte Carlo (MC) simulations. Contrary to a more conventional scenario with single active phase for 1d models…
We describe a mathematical modeling of the digestion in the small intestine. The main interest of our work is to consider, at the same time, different aspects of the digestion i.e. the transport of the bolus all along the intestine,…
We propose a whole-body model of the metabolism in man as well as a generalized approach for modeling metabolic networks. Using this approach, we are able to write a large metabolic network in a systematic and compact way. We demonstrate…